diff --git a/.dlt/config.toml b/.dlt/config.toml
index 2e36ec31..c86b2b79 100644
--- a/.dlt/config.toml
+++ b/.dlt/config.toml
@@ -10,7 +10,7 @@ log_format = "JSON"
 # default: 60
 request_timeout = 60
 # default: 5
-request_max_attempts = 2
+request_max_attempts = 10
 # default: 1
 request_backoff_factor = 1.5
 # default: 300
diff --git a/.github/workflows/docker_build.yaml b/.github/workflows/docker_build.yaml
index be606ea4..5949ec5b 100644
--- a/.github/workflows/docker_build.yaml
+++ b/.github/workflows/docker_build.yaml
@@ -6,12 +6,8 @@ on:
     workflow_call:
 
     push:
-        branches: ["main"]
-        # Publish semver tags as releases.
-        tags:
-            - "v[0-9]+.[0-9]+.[0-9]+"
-            - "[0-9]+.[0-9]+.[0-9]+"
-            - "[0-9]+.[0-9]+.[0-9]+-*"
+        branches:
+            - main
     pull_request:
         types:
             - opened
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f8eb20ac..98287e6b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -3,8 +3,7 @@ permissions:
   contents: read
 
 on:
-  push:
-    branches: [main, develop]
+  workflow_call:
 
   pull_request:
     types:
diff --git a/.github/workflows/trivy.yaml b/.github/workflows/trivy.yaml
index d09c170e..aa6735f4 100644
--- a/.github/workflows/trivy.yaml
+++ b/.github/workflows/trivy.yaml
@@ -6,8 +6,7 @@
 name: trivy
 
 on:
-    push:
-        branches: [main, develop]
+    workflow_call:
 
     pull_request:
         types:
diff --git a/README.md b/README.md
index 98aba015..4ecc8b96 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,7 @@ Repo for CDM input data loading and wrangling
   - [Loading genomes, contigs, and features](#loading-genomes-contigs-and-features)
   - [Running bbmap stats and checkm2 on genome or contigset files](#running-bbmap-stats-and-checkm2-on-genome-or-contigset-files)
   - [Changelog](#changelog)
+    - [v0.1.7](#v017)
     - [v0.1.6](#v016)
     - [v0.1.5](#v015)
     - [v0.1.4](#v014)
@@ -171,6 +172,10 @@ where `path/to/genome_paths_file.json` specifies the path to the genome paths fi
 
 ## Changelog
 
+### v0.1.7
+
+- Add in AllTheBacteria file download client.
+
 ### v0.1.6
 
 - Make NCBI REST API client more resilient to errors and ensure existing imports are not lost.
diff --git a/pyproject.toml b/pyproject.toml
index c90538a0..b5cce288 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "cdm-data-loaders"
-version = "0.1.6"
+version = "0.1.7"
 description = "Data loaders and wranglers for the CDM."
 requires-python = ">= 3.13"
 readme = "README.md"
@@ -16,16 +16,18 @@ dependencies = [
     "delta-spark>=4.1.0",
     "dlt[deltalake,duckdb,filesystem,parquet]>=1.22.2",
     "frictionless[aws]>=5.18.1",
+    "frozendict>=2.4.7",
     "lxml>=6.0.2",
     "pydantic>=2.12.5",
     "pydantic-settings>=2.12.0",
+    "tqdm>=4.67.3",
 ]
 
 [project.scripts]
-# idmapping = "cdm_data_loaders.parsers.uniprot.idmapping:cli"
+all_the_bacteria = "cdm_data_loaders.pipelines.all_the_bacteria:cli"
+ncbi_rest_api = "cdm_data_loaders.pipelines.ncbi_rest_api:cli"
 uniprot = "cdm_data_loaders.pipelines.uniprot_kb:cli"
 uniref = "cdm_data_loaders.pipelines.uniref:cli"
-ncbi_rest_api = "cdm_data_loaders.pipelines.ncbi_rest_api:cli"
 
 [dependency-groups]
 dev = [
@@ -48,11 +50,6 @@ xml = [
 ]
 
 [project.optional-dependencies]
-# for s3 interactions -- see utils/s3.py for more details
-s3 = [
-    "boto3[crt]>=1.42.0",
-    "tqdm>=4.67.3",
-]
 
 [tool.ruff]
 line-length = 120
diff --git a/scripts/entrypoint.sh b/scripts/entrypoint.sh
index 74d90521..2be0475f 100755
--- a/scripts/entrypoint.sh
+++ b/scripts/entrypoint.sh
@@ -3,7 +3,7 @@ set -euo pipefail
 
 # Ensure at least one argument is provided
 if [ "$#" -eq 0 ]; then
-  echo "Usage: $0 {uniref|uniprot|ncbi_rest_api|xml_split|test} [args...]"
+  echo "Usage: $0 {all_the_bacteria|ncbi_rest_api|uniprot|uniref|xml_split|test} [args...]"
   exit 1
 fi
 
@@ -11,21 +11,25 @@ cmd="$1"
 shift
 
 case "$cmd" in
-  xml_split)
-    # Run the xml_file_splitter app
-    exec /usr/bin/tini -- xml_file_splitter "$@"
+  all_the_bacteria)
+    # All the Bacteria file importer
+    exec /usr/bin/tini -- uv run --no-sync all_the_bacteria "$@"
     ;;
-  uniref)
-    # Run the uniref pipeline with any additional arguments
-    exec /usr/bin/tini -- uv run --no-sync uniref "$@"
+  ncbi_rest_api)
+    # Run the NCBI datasets API importer
+    exec /usr/bin/tini -- uv run --no-sync ncbi_rest_api "$@"
     ;;
   uniprot)
     # Run the uniprot pipeline with any additional arguments
     exec /usr/bin/tini -- uv run --no-sync uniprot "$@"
     ;;
-  ncbi_rest_api)
-    # Run the NCBI datasets API importer
-    exec /usr/bin/tini -- uv run --no-sync ncbi_rest_api "$@"
+  uniref)
+    # Run the uniref pipeline with any additional arguments
+    exec /usr/bin/tini -- uv run --no-sync uniref "$@"
+    ;;
+  xml_split)
+    # Run the xml_file_splitter app
+    exec /usr/bin/tini -- xml_file_splitter "$@"
     ;;
   test)
     # run the tests
@@ -35,7 +39,7 @@ case "$cmd" in
     exec /usr/bin/tini -- /bin/bash
     ;;
   *)
-    echo "Error: unknown command '$cmd'; valid commands are 'uniref', 'uniprot', 'ncbi_rest_api', or 'xml_split'." >&2
+    echo "Error: unknown command '$cmd'; valid commands are 'all_the_bacteria', 'ncbi_rest_api', 'uniprot', 'uniref', or 'xml_split'." >&2
     exit 1
     ;;
 esac
diff --git a/src/cdm_data_loaders/pipelines/all_the_bacteria.py b/src/cdm_data_loaders/pipelines/all_the_bacteria.py
new file mode 100644
index 00000000..bb32836a
--- /dev/null
+++ b/src/cdm_data_loaders/pipelines/all_the_bacteria.py
@@ -0,0 +1,221 @@
+"""All The Bacteria bulk data downloader.
+
+Project documentation: https://allthebacteria.org/
+
+Batch downloading from OSF: https://allthebacteria.org/docs/osf_downloads/
+
+all_atb_files.tsv: https://osf.io/xv7q9/files/r6gcp (or Rg6cp, casing varies)
+
+"""
+
+import csv
+import logging
+import re
+from collections.abc import Generator
+from pathlib import Path
+from typing import Any
+
+import dlt
+from dlt.extract.items import DataItemWithMeta
+from dlt.sources.helpers.rest_client.client import RESTClient
+from frozendict import frozendict
+from pydantic import AliasChoices, Field
+from pydantic_settings import SettingsConfigDict
+
+from cdm_data_loaders.pipelines.core import (
+    run_cli,
+    run_pipeline,
+)
+from cdm_data_loaders.pipelines.cts_defaults import DEFAULT_SETTINGS_CONFIG_DICT, CtsSettings
+from cdm_data_loaders.utils.download.sync_client import FileDownloader
+
+logger = logging.getLogger("dlt")
+
+
+DATASET_NAME = "all_the_bacteria"
+ALL_FILES_TSV_FILE_ID = "R6gcp"
+ATB_VERSION = "2025-05"
+
+ARG_ALIASES = frozendict(
+    {
+        "version": ["-v", "--version"],
+    }
+)
+
+
+class AtbSettings(CtsSettings):
+    """Configuration for running the AllTheBacteria import pipeline."""
+
+    model_config = SettingsConfigDict(**DEFAULT_SETTINGS_CONFIG_DICT, cli_prog_name="all_the_bacteria")
+
+    version: str = Field(
+        default=ATB_VERSION,
+        description="Name of the current AllTheBacteria version",
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["version"]]),
+    )
+
+    @property
+    def raw_data_dir(self) -> str:
+        """Directory in which to save the raw data files that are downloaded.
+
+        Set to the output directory / "raw_data" / version.
+        """
+        return str(Path(self.output) / "raw_data" / self.version)
+
+
+# project parts needed:
+PROJECT_PARTS = ["Annotation/Bakta", "Assembly", "Metadata"]
+
+PROJECT_PART_REGEX = re.compile(f"^AllTheBacteria/({'|'.join(PROJECT_PARTS)})")
+
+EXPECTED_ATB_FIELDNAMES = ["project", "project_id", "filename", "url", "md5", "size(MB)"]
+REQUIRED_ATB_FIELDNAMES = {"project", "filename", "url", "md5"}
+
+
+def download_atb_index_tsv(settings: AtbSettings) -> Path:
+    """Download the ATB file index TSV file from the OSF and save it to disk.
+
+    :param settings: pipeline config
+    :type settings: Settings
+    :raises RuntimeError: if the download URL cannot be found
+    :return: path to the downloaded file
+    :rtype: Path
+    """
+    # make sure that the directory structure to save the file in can be written to
+    raw_data_dir = Path(settings.raw_data_dir)
+    raw_data_dir.mkdir(parents=True, exist_ok=True)
+
+    # get the all_atb_files.tsv file info from the OSF API and retrieve the download link
+    osf_client = RESTClient(
+        base_url="https://api.osf.io/v2/",
+        headers={"accept": "application/json"},
+        data_selector="data",
+    )
+    resp = osf_client.get(f"https://api.osf.io/v2/files/{ALL_FILES_TSV_FILE_ID}/")
+    resp.raise_for_status()
+
+    resp_json = resp.json()
+    all_files_tsv_download = resp_json.get("data", {}).get("links", {}).get("download")
+    if all_files_tsv_download is None:
+        logger.error("Could not find download URL in OSF API response:")
+        logger.error(resp_json)
+        err_msg = f"Could not find download URL in response from 'https://api.osf.io/v2/files/{ALL_FILES_TSV_FILE_ID}/'"
+        raise RuntimeError(err_msg)
+
+    atb_files_tsv = raw_data_dir / "all_atb_files.tsv"
+    # download the file listing and save it
+    FileDownloader().download(all_files_tsv_download, atb_files_tsv)
+    return atb_files_tsv
+
+
+def get_file_download_links(atb_files_tsv: Path) -> Generator[list[dict[str, Any]], Any]:
+    """Parse the ATB file index TSV and to yield a list of files to download.
+
+    :param atb_files_tsv: path to the ATB file index TSV file
+    :type atb_files_tsv: Path
+    :yield: list of fields to download
+    :rtype: Generator[list[dict[str, Any]], Any]
+    """
+    with atb_files_tsv.open() as index_file:
+        reader = csv.DictReader(index_file, delimiter="\t")
+        all_lines = list(reader)
+        if not all_lines:
+            err_msg = f"No valid TSV data found in {atb_files_tsv!s}"
+            logger.error(err_msg)
+            raise RuntimeError(err_msg)
+
+        if reader.fieldnames != EXPECTED_ATB_FIELDNAMES:
+            err_msg = f"ATB file index TSV headers have changed.\nExpected: {EXPECTED_ATB_FIELDNAMES}\nGot: {reader.fieldnames}"
+            logger.warning(err_msg)
+            # do we have the essentials? project, filename, url, md5
+            missing_required_fields = [f for f in REQUIRED_ATB_FIELDNAMES if f not in (reader.fieldnames or [])]
+            if missing_required_fields:
+                err_msg = f"Missing required ATB file index TSV headers: {sorted(missing_required_fields)}"
+                logger.error(err_msg)
+                raise RuntimeError(err_msg)
+
+        files_to_download = [row for row in all_lines if PROJECT_PART_REGEX.match(row["project"])]
+
+        yield files_to_download
+
+
+def osf_file_downloader(settings: AtbSettings, atb_file_list: list[dict[str, Any]]) -> Generator[DataItemWithMeta, Any]:
+    """Download files from OSF to the local storage space.
+
+    :param settings: pipeline config
+    :type settings: Settings
+    :param atb_file_list: list of dictionaries
+    :type atb_file_list: list[dict[str, Any]]
+    """
+    client = FileDownloader()
+    raw_data_dir = Path(settings.raw_data_dir)
+    successful_downloads = []
+    for f in atb_file_list:
+        try:
+            save_path = raw_data_dir / f["filename"]
+            client.download(f["url"], save_path, expected_checksum=f["md5"], checksum_fn="md5")
+            f["path"] = str(save_path)
+            successful_downloads.append(f)
+        except Exception as e:
+            # do something!
+            err_msg = f"Could not download file from {f['url']}: {e!s}"
+            logger.exception(err_msg)
+            continue
+
+    yield dlt.mark.with_table_name(successful_downloads, "downloaded_files")
+
+
+@dlt.resource(name="atb_file_list")
+def atb_file_list(settings: AtbSettings) -> Generator[list[dict[str, Any]], Any, Any]:
+    """Generate a list of files to download from the list of all ATB files."""
+    atb_files_tsv = download_atb_index_tsv(settings)
+    return get_file_download_links(atb_files_tsv)
+
+
+@dlt.transformer(name="file_downloader", data_from=atb_file_list, parallelized=True)
+def file_downloader(
+    atb_file_list: list[dict[str, Any]],
+    settings: AtbSettings,
+) -> Generator[DataItemWithMeta, Any]:
+    """Download ATB files to disk.
+
+    :param settings: pipeline config
+    :type settings: Settings
+    :param atb_file_list: list of files to download
+    :type atb_file_list: list[dict[str, Any]]
+    :return: output of the osf_file_downloader
+    :rtype: Generator[DataItemWithMeta]
+    """
+    return osf_file_downloader(settings, atb_file_list)
+
+
+def run_atb_pipeline(settings: AtbSettings) -> None:
+    """Run the AllTheBacteria pipeline.
+
+    :param settings: configuration for the pipeline
+    :type settings: AtbSettings
+    """
+    atb_file_list.bind(settings)
+    file_downloader.bind(settings)
+
+    pipeline_kwargs: dict[str, Any] = {
+        "pipeline_name": DATASET_NAME,
+        "dataset_name": DATASET_NAME,
+    }
+
+    run_pipeline(
+        settings=settings,
+        resource=file_downloader,
+        destination_kwargs={"max_table_nesting": 0},
+        pipeline_kwargs=pipeline_kwargs,
+        pipeline_run_kwargs=None,
+    )
+
+
+def cli() -> None:
+    """CLI interface for the AllTheBacteria importer pipeline."""
+    run_cli(AtbSettings, run_atb_pipeline)
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/src/cdm_data_loaders/pipelines/core.py b/src/cdm_data_loaders/pipelines/core.py
index 81dc3f7d..3d821f59 100644
--- a/src/cdm_data_loaders/pipelines/core.py
+++ b/src/cdm_data_loaders/pipelines/core.py
@@ -1,6 +1,8 @@
 """Common reusable pipeline elements."""
 
 import datetime
+import logging
+import os
 from collections.abc import Callable, Generator
 from typing import Any
 
@@ -8,36 +10,64 @@
 from dlt.common.runtime.slack import send_slack_message
 from dlt.extract.items import DataItemWithMeta
 from pydantic import ValidationError
-from pydantic_settings import BaseSettings, SettingsError
+from pydantic_settings import SettingsError
 
-from cdm_data_loaders.pipelines.cts_defaults import DEFAULT_BATCH_SIZE, BatchedFileInputSettings, CtsDefaultSettings
-from cdm_data_loaders.utils.cdm_logger import get_cdm_logger
+from cdm_data_loaders.pipelines.cts_defaults import DEFAULT_BATCH_SIZE, BatchedFileInputSettings, CtsSettings
 from cdm_data_loaders.utils.file_system import BatchCursor
 from cdm_data_loaders.utils.xml_utils import stream_xml_file
 
-logger = get_cdm_logger()
+logger = logging.getLogger("dlt")
 
 
-def run_cli(settings_cls: type[BaseSettings], pipeline_fn: Callable[[Any], None]) -> None:
+def construct_env_var() -> None:
+    """Use environment variables to construct a new environment variable."""
+    b_var = os.environ.get("VARIABLE_B")
+    t_var = os.environ.get("VARIABLE_T")
+    char_str = os.environ.get("CHAR_STR")
+    if all([b_var, t_var, char_str]):
+        os.environ["RUNTIME__SLACK_INCOMING_HOOK"] = f"https://hooks.slack.com/services/{b_var}/{t_var}/{char_str}/"
+
+
+def sync_configs(settings: CtsSettings, dlt_config: Any) -> None:
+    """Sync the dlt config with the config derived from the CLI settings."""
+    dlt_config["normalize.data_writer.disable_compression"] = settings.dev_mode
+    # make sure that the destination bucket_url is set correctly
+    dlt_config[f"destination.{settings.use_destination}.bucket_url"] = settings.output
+
+
+def dump_settings(settings: CtsSettings) -> None:
+    """Dump the pipeline settings to the logger."""
+    settings_minus_dlt_config = settings.model_dump(exclude={"dlt_config"})
+    logger.info("Pipeline settings:")
+    logger.info(settings_minus_dlt_config)
+
+
+def run_cli(settings_cls: type[CtsSettings], pipeline_fn: Callable[[Any], None]) -> None:
     """Generic CLI entry point for any pipeline.
 
     :param settings_cls: the Settings class to instantiate
     :param pipeline_fn: the run_pipeline function to call with the config
     """
+    # piece together env vars
+    construct_env_var()
+
+    # instantiate the config
     try:
-        config = settings_cls()
-    except (SettingsError, ValidationError) as e:
-        print(f"Error initialising config: {e}")
+        settings = settings_cls(dlt_config=dlt.config)
+        sync_configs(settings, dlt.config)
+    except (SettingsError, ValidationError, ValueError):
+        logger.exception("Error initialising config")
         raise
-    except Exception as e:
-        print(f"Unexpected error setting up config: {e}")
+    except Exception:
+        logger.exception("Unexpected error setting up config")
         raise
 
-    pipeline_fn(config)
+    dump_settings(settings)
+    pipeline_fn(settings)
 
 
 def run_pipeline(
-    config: CtsDefaultSettings,
+    settings: CtsSettings,
     resource: Any,  # noqa: ANN401
     destination_kwargs: dict[str, Any] | None = None,
     pipeline_kwargs: dict[str, Any] | None = None,
@@ -45,8 +75,8 @@ def run_pipeline(
 ) -> None:
     """Execute a dlt pipeline.
 
-    :param config: pipeline config with output and destination
-    :type config: BatchedFileInputSettings
+    :param settings: pipeline config with output and destination
+    :type settings: BatchedFileInputSettings
     :param resource: dlt resource to run
     :type resource: Any
     :param destination_kwargs: keyword arguments for the dlt destination
@@ -56,11 +86,20 @@ def run_pipeline(
     :param pipeline_run_kwargs: keyword arguments for the dlt pipeline run
     :type pipeline_run_kwargs: dict[str, Any] | None
     """
-    if config.output:
-        dlt.config[f"destination.{config.destination}.bucket_url"] = config.output
+    if not pipeline_kwargs:
+        pipeline_kwargs = {}
+
+    # set the output directory for all the pipeline gubbins
+    if settings.pipeline_dir:
+        pipeline_kwargs["pipelines_dir"] = settings.pipeline_dir
+
+    # update dev mode
+    if settings.dev_mode:
+        pipeline_kwargs["dev_mode"] = settings.dev_mode
+
+    destination = dlt.destination(settings.use_destination, **(destination_kwargs or {}))
 
-    destination = dlt.destination(config.destination, **(destination_kwargs or {}))
-    pipeline = dlt.pipeline(destination=destination, **(pipeline_kwargs or {}))
+    pipeline = dlt.pipeline(destination=destination, **pipeline_kwargs)
 
     slack_hook: str | None = pipeline.runtime_config.slack_incoming_hook
 
@@ -83,24 +122,28 @@ def run_pipeline(
 
 
 def stream_xml_file_resource(
-    config: BatchedFileInputSettings,
+    settings: BatchedFileInputSettings,
     xml_tag: str,
     parse_fn: Callable,
     log_interval: int = 1000,
 ) -> Generator[DataItemWithMeta, Any]:
     """Core generator shared by XML-based dlt pipeline resources.
 
-    :param config: pipeline config with input_dir and start_at
+    :param settings: pipeline config with input_dir and start_at
+    :type settings: BatchedFileInputSettings
     :param xml_tag: XML element tag to stream
+    :type xml_tag: str
     :param parse_fn: callable(entry, timestamp, file_path) -> dict[str, rows]
+    :type parse_fn: Callable
     :param log_interval: log a progress message every N entries
+    :type log_interval: int
     """
     timestamp = datetime.datetime.now(tz=datetime.UTC)
     batch_params: dict[str, Any] = {}
-    if config.start_at:
-        batch_params["start_at"] = config.start_at
+    if settings.start_at:
+        batch_params["start_at"] = settings.start_at
 
-    batcher = BatchCursor(config.input_dir, batch_size=DEFAULT_BATCH_SIZE, **batch_params)
+    batcher = BatchCursor(settings.input_dir, batch_size=DEFAULT_BATCH_SIZE, **batch_params)
     while files := batcher.get_batch():
         for file_path in files:
             logger.info("Reading from %s", str(file_path))
diff --git a/src/cdm_data_loaders/pipelines/cts_defaults.py b/src/cdm_data_loaders/pipelines/cts_defaults.py
index d609907b..5f59ff91 100644
--- a/src/cdm_data_loaders/pipelines/cts_defaults.py
+++ b/src/cdm_data_loaders/pipelines/cts_defaults.py
@@ -1,62 +1,172 @@
 """Common defaults for running pipelines on the KBase CTS."""
 
-from pydantic import AliasChoices, Field, field_validator
-from pydantic_settings import BaseSettings, SettingsConfigDict
+from pathlib import Path
+from typing import Any, Self
+
+import dlt.common.configuration.accessors
+from frozendict import frozendict
+from pydantic import AliasChoices, Field, computed_field, field_validator, model_validator
+from pydantic_settings import BaseSettings, CliSuppress, SettingsConfigDict
 
 INPUT_MOUNT = "/input_dir"
 OUTPUT_MOUNT = "/output_dir"
 
 VALID_DESTINATIONS = ["local_fs", "s3"]
 DEFAULT_BATCH_SIZE = 50
+DEFAULT_START_AT = 0
+
+# TODO: frozendict can be moved to the stdlib implementation when py 3.15 is released.
+
+
+DEFAULT_CTS_SETTINGS = frozendict(
+    {
+        "dev_mode": False,
+        "input_dir": INPUT_MOUNT,
+        # N.b. this gets replaced by destination.local_fs.bucket_url
+        "output": "",
+        "use_destination": "local_fs",
+        "use_output_dir_for_pipeline_metadata": False,
+    }
+)
+
+DEFAULT_BATCH_FILE_SETTINGS = frozendict(
+    {
+        **DEFAULT_CTS_SETTINGS,
+        "start_at": DEFAULT_START_AT,
+    }
+)
+
+
+ARG_ALIASES = frozendict(
+    {
+        "batch_size": ["-b", "--batch_size", "--batch-size"],
+        "dev_mode": ["--dev_mode", "--dev-mode", "--dev"],
+        "input_dir": ["-i", "--input_dir", "--input-dir"],
+        "output": ["-o", "--output"],
+        "start_at": ["-s", "--start_at", "--start-at"],
+        "use_destination": ["-d", "--use_destination", "--use-destination"],
+        "use_output_dir_for_pipeline_metadata": [
+            "-p",
+            "--use_output_dir_for_pipeline_metadata",
+            "--use-output-dir-for-pipeline-metadata",
+        ],
+    }
+)
+
+DEFAULT_SETTINGS_CONFIG_DICT = frozendict(
+    {
+        "cli_parse_args": True,
+        "cli_exit_on_error": False,
+        "cli_ignore_unknown_args": True,
+        "str_strip_whitespace": True,
+    }
+)
 
 
-class CtsDefaultSettings(BaseSettings):
+class CtsSettings(BaseSettings):
     """Configuration for running a basic import pipeline."""
 
-    model_config = SettingsConfigDict(
-        cli_parse_args=True,
-        cli_exit_on_error=False,
-        cli_ignore_unknown_args=True,
+    model_config = SettingsConfigDict(**DEFAULT_SETTINGS_CONFIG_DICT)
+
+    dev_mode: bool = Field(
+        default=DEFAULT_CTS_SETTINGS["dev_mode"],
+        description="Whether to run the pipeline in dev mode, which saves raw API responses to disk and disables compression for easier debugging.",
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["dev_mode"]]),
     )
     input_dir: str = Field(
-        default=INPUT_MOUNT,
-        description="Location of directory containing UniRef XML files to import",
+        default=DEFAULT_CTS_SETTINGS["input_dir"],
+        description="Location of directory containing file(s) to import",
         # explicitly allow both kebab case and snake case
-        validation_alias=AliasChoices("i", "input_dir", "input-dir", "input_dir"),
-    )
-    destination: str = Field(
-        default="local_fs",
-        description=f"Destination configuration to use for data output. Choices: {VALID_DESTINATIONS}",
-        validation_alias=AliasChoices("d", "destination"),
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["input_dir"]]),
     )
-    output: str | None = Field(
-        default=None,
+    output: str = Field(
+        default=DEFAULT_CTS_SETTINGS["output"],
         description="Location to save imported data to, if different from the default supplied by the destination config",
-        validation_alias=AliasChoices("o", "output"),
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["output"]]),
+    )
+    use_destination: str = Field(
+        default=DEFAULT_CTS_SETTINGS["use_destination"],
+        description=f"DLT destination configuration to use for data output. Choices: {VALID_DESTINATIONS}",
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["use_destination"]]),
+    )
+    use_output_dir_for_pipeline_metadata: bool = Field(
+        default=DEFAULT_CTS_SETTINGS["use_output_dir_for_pipeline_metadata"],
+        description="If true, use the output directory for pipeline metadata.",
+        validation_alias=AliasChoices(
+            *[alias.strip("-") for alias in ARG_ALIASES["use_output_dir_for_pipeline_metadata"]]
+        ),
     )
+    # this should really just be _Accessor but leaving it as-is for ease of testing
+    dlt_config: CliSuppress[dlt.common.configuration.accessors._Accessor | dict[str, Any]] = Field(
+        description="DLT configuration for the pipeline.",
+    )
+
+    @model_validator(mode="after")
+    def reconcile_with_dlt_config(self) -> Self:
+        """Update dlt.config based on the current state of the settings."""
+        # validate destination
+        all_destinations = self.dlt_config.get("destination") or {}  # type: ignore[reportArgumentType]
+        if not all_destinations:
+            err_msg = "No valid destinations found in dlt configuration."
+            raise ValueError(err_msg)
 
-    @field_validator("destination")
+        if self.use_destination not in all_destinations:
+            err_msg = f"use_destination must be one of {sorted(all_destinations)}, got '{self.use_destination}'"
+            raise ValueError(err_msg)
+
+        if not self.output:
+            if not self.dlt_config.get(f"destination.{self.use_destination}.bucket_url"):  # type: ignore[reportArgumentType]
+                err_msg = f"No bucket_url specified for destination {self.use_destination}"
+                raise ValueError(err_msg)
+
+            self.output = self.dlt_config[f"destination.{self.use_destination}.bucket_url"]
+
+        return self
+
+    @field_validator("dlt_config", mode="before")
     @classmethod
-    def validate_destination(cls, v: str) -> str:
-        """Validate the destination against valid choices.
-
-        :param v: destination specified
-        :type v: str
-        :raises ValueError: if the destination is not valid
-        :return: valid destination
-        :rtype: str
-        """
-        if v not in VALID_DESTINATIONS:
-            err_msg = f"destination must be one of {VALID_DESTINATIONS}, got '{v}'"
+    def validate_dlt_config(cls, dlt_config: Any) -> Any:
+        """Perform some rudimentary validation on the incoming dlt config."""
+        if dlt_config is None:
+            err_msg = "dlt_config must be defined"
             raise ValueError(err_msg)
-        return v
+
+        return dlt_config
+
+    @field_validator("input_dir", "output", mode="after")
+    @classmethod
+    def validate_dir_path(cls, value: str) -> str:
+        """Remove any trailing slashes from directory paths."""
+        if value == "/":
+            return value
+        return value.rstrip("/")
+
+    @computed_field
+    @property
+    def raw_data_dir(self) -> str:
+        """Directory in which to save the raw data files that are downloaded.
+
+        If not set, defaults to a 'raw_data' directory within the output directory after reconciling with dlt config.
+        """
+        return str(Path(self.output or "") / "raw_data")
+
+    @computed_field
+    @property
+    def pipeline_dir(self) -> str | None:
+        """Custom directory to save pipeline metadata to.
+
+        If use_output_dir_for_pipeline_metadata is true, this defaults to a `.dlt_conf` directory within the output directory.
+        """
+        if self.use_output_dir_for_pipeline_metadata:
+            return str(Path(self.output or "") / ".dlt_conf")
+        return None
 
 
-class BatchedFileInputSettings(CtsDefaultSettings):
+class BatchedFileInputSettings(CtsSettings):
     """Settings object for an importer that deals with batches of files."""
 
     start_at: int = Field(
-        default=0,
+        default=DEFAULT_BATCH_FILE_SETTINGS["start_at"],
         description="File to start import at",
-        validation_alias=AliasChoices("s", "start", "start-at", "start_at"),
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIASES["start_at"]]),
     )
diff --git a/src/cdm_data_loaders/pipelines/ncbi_rest_api.py b/src/cdm_data_loaders/pipelines/ncbi_rest_api.py
index a9b00f8d..f41d0acf 100644
--- a/src/cdm_data_loaders/pipelines/ncbi_rest_api.py
+++ b/src/cdm_data_loaders/pipelines/ncbi_rest_api.py
@@ -17,17 +17,15 @@
 from dlt.sources.helpers.rest_client.paginators import (
     JSONResponseCursorPaginator,
 )
-from pydantic import AliasChoices, Field, model_validator
-from pydantic_settings import CliSuppress, SettingsConfigDict
+from pydantic import AliasChoices, Field
+from pydantic_settings import SettingsConfigDict
 from requests.exceptions import HTTPError
 
 from cdm_data_loaders.pipelines.core import (
     run_cli,
     run_pipeline,
 )
-from cdm_data_loaders.pipelines.cts_defaults import (
-    BatchedFileInputSettings,
-)
+from cdm_data_loaders.pipelines.cts_defaults import DEFAULT_SETTINGS_CONFIG_DICT, CtsSettings
 from cdm_data_loaders.utils.file_system import BatchCursor
 
 DATASET_NAME = "ncbi_rest_api"
@@ -41,64 +39,28 @@
 ANNOTATION = "annotation"
 ERROR = "error"
 
-dlt_logger = logging.getLogger("dlt")
+logger = logging.getLogger("dlt")
 
 REST_CLIENT_HOOKS = {}
 
+ARG_ALIAS_BATCH_SIZE = ["-b", "--batch-size", "--batch_size"]
+
 
-class Settings(BatchedFileInputSettings):
+class NcbiSettings(CtsSettings):
     """Configuration for running the NCBI REST API import pipeline."""
 
-    model_config = SettingsConfigDict(
-        cli_parse_args=True,
-        cli_prog_name="ncbi_rest_api",
-        cli_exit_on_error=False,
-        cli_ignore_unknown_args=True,
-    )
+    model_config = SettingsConfigDict(**DEFAULT_SETTINGS_CONFIG_DICT, cli_prog_name="ncbi_rest_api")
 
     batch_size: int = Field(
         default=MAX_RESULTS_PER_PAGE,
         description="Number of IDs to send in each request to the NCBI REST API.",
-        validation_alias=AliasChoices("b", "batch-size", "batch_size"),
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in ARG_ALIAS_BATCH_SIZE]),
         ge=1,
         le=MAX_RESULTS_PER_PAGE,
     )
 
-    pipeline_dir: CliSuppress[Path | None] = Field(
-        default=None, description="Custom directory to save pipeline metadata to."
-    )
-
-    use_output_dir_for_pipeline_metadata: bool = Field(
-        default=False,
-        description="If true, use the output directory for pipeline metadata.",
-        validation_alias=AliasChoices("p", "pipeline-dir", "pipeline_dir", "use_output_dir_for_pipeline_metadata"),
-    )
-
-    dev_mode: bool = Field(
-        default=False,
-        description="Whether to run the pipeline in dev mode, which saves raw API responses to disk and disables compression for easier debugging.",
-        validation_alias=AliasChoices("dev", "dev_mode", "dev-mode"),
-    )
 
-    @model_validator(mode="after")
-    def set_output_dir(self) -> "Settings":
-        """Set a default for the output directory if not set."""
-        if self.output is None:
-            self.output = dlt.config[f"destination.{self.destination}.bucket_url"]
-        else:
-            dlt.config[f"destination.{self.destination}.bucket_url"] = self.output
-        return self
-
-    @model_validator(mode="after")
-    def set_pipeline_dir_default(self) -> "Settings":
-        """Set a default for the pipeline directory if not set."""
-        if self.use_output_dir_for_pipeline_metadata:
-            p_dir = self.output
-            self.pipeline_dir = Path(p_dir) / ".dlt_conf"  # type: ignore[reportArgumentType]
-        return self
-
-
-def generate_file_path_name_from_url(config: Settings, url_string: str) -> Path:
+def generate_file_path_name_from_url(settings: NcbiSettings, url_string: str) -> Path:
     """Given an NCBI URL, generate a save directory and file name for the raw HTTP responses.
 
     :param url_string: the URL
@@ -106,7 +68,7 @@ def generate_file_path_name_from_url(config: Settings, url_string: str) -> Path:
     :return: path for the save dir
     :rtype: Path
     """
-    raw_data_dir = Path(config.output) / "raw_responses"  # type: ignore[reportArgumentType]
+    raw_data_dir = Path(settings.raw_data_dir) / "api_responses"  # type: ignore[reportArgumentType]
     url = urlparse(url_string)
     # retrieve the page token
     page_token = "".join(parse_qs(url.query).get("page_token", []))
@@ -123,7 +85,7 @@ def generate_file_path_name_from_url(config: Settings, url_string: str) -> Path:
     return save_dir / file_name
 
 
-def save_raw_response(config: Settings, response: Response, *_: Any, **__: Any) -> Response:  # noqa: ANN401
+def save_raw_response(settings: NcbiSettings, response: Response, *_: Any, **__: Any) -> Response:  # noqa: ANN401
     """Save the response content to disk.
 
     :param response: HTTP Response object
@@ -131,7 +93,7 @@ def save_raw_response(config: Settings, response: Response, *_: Any, **__: Any)
     :return: the response
     :rtype: Response
     """
-    file_path = generate_file_path_name_from_url(config, response.url)
+    file_path = generate_file_path_name_from_url(settings, response.url)
     file_path.write_bytes(response.content)
     return response
 
@@ -228,7 +190,7 @@ def get_dataset_reports(assembly_id_list: list[str]) -> dict[str, None | dict[st
     if not assembly_id_list:
         return {}
 
-    dlt_logger.info("fetching dataset reports for:\n%s", ", ".join(sorted(assembly_id_list)))
+    logger.info("fetching dataset reports for:\n%s", ", ".join(sorted(assembly_id_list)))
     assembly_dataset_reports = []
 
     for page in ncbi_genome_client.paginate(
@@ -249,7 +211,7 @@ def get_dataset_reports(assembly_id_list: list[str]) -> dict[str, None | dict[st
 
 def get_annotation_report(assembly_id: str) -> list[dict[str, Any]] | None:
     """Fetch the annotation report for an assembly from the NCBI datasets REST API."""
-    dlt_logger.info("fetching annotation report for %s", assembly_id)
+    logger.info("fetching annotation report for %s", assembly_id)
     page_data = []
 
     for page in ncbi_genome_client.paginate(
@@ -265,27 +227,7 @@ def get_annotation_report(assembly_id: str) -> list[dict[str, Any]] | None:
     return page_data or None
 
 
-@dlt.resource(name="assembly_list")
-def assembly_list(config: Settings) -> Generator[list[str], Any, Any]:
-    """List of assemblies to fetch."""
-    batcher = BatchCursor(config.input_dir, batch_size=1)
-    while files := batcher.get_batch():
-        for file_path in files:
-            with file_path.open() as f:
-                while next_chunk := list(islice(f, config.batch_size)):
-                    yield [line.strip() for line in next_chunk if line.strip()]
-
-
-@dlt.transformer(name="assembly_reports", data_from=assembly_list, max_table_nesting=0)
-def assembly_reports(
-    assembly_id_list: list[str],
-) -> Generator[dict[str, dict[str, dict[str, Any]] | list[dict[str, Any]]], Any]:
-    """Fetch reports for a list of assemblies from the NCBI datasets REST API."""
-    yield get_assembly_reports(assembly_id_list)
-
-
-@dlt.transformer(name="assembly_report_parser", data_from=assembly_reports, max_table_nesting=0)
-def assembly_report_parser(
+def assemble_assembly_reports(
     assembly_reports: dict[str, dict[str, Any]],
 ) -> Generator[DataItemWithMeta, Any]:
     """Parse and export assembly data from the REST API.
@@ -302,48 +244,75 @@ def assembly_report_parser(
     annotation_reports: dict[str, list[dict[str, Any]]] = assembly_reports.get(ANNOTATION)  # type: ignore[reportAssignmentType]
     error_reports: list[dict[str, Any]] = assembly_reports.get(ERROR)  # type: ignore[reportAssignmentType]
 
-    if error_reports:
-        yield dlt.mark.with_table_name(error_reports, "ncbi_import_error")
-
     # yield the raw data to save as tables
-    yield dlt.mark.with_table_name(
-        [{"assembly_id": assembly_id, **(report or {})} for assembly_id, report in dataset_reports.items()],
-        f"{DATASET}_report",
-    )
+    # every assembly_id in dataset_reports should have a row in the dataset_report table
+    # even if the value is None due to an error or invalid ID
+    if dataset_reports:
+        yield dlt.mark.with_table_name(
+            [{"assembly_id": assembly_id, **(report or {})} for assembly_id, report in dataset_reports.items()],
+            f"{DATASET}_report",
+        )
+
+    # save the rows from the annotation reports
+    # only assemblies with annotation reports have rows in the annotation_report table
     tr_annotation_rows = [
         {"assembly_id": aid, **report}
         for aid, report_list in annotation_reports.items()
         for report in (report_list or [])
     ]
-    # save the rows from the annotation reports
-    yield dlt.mark.with_table_name(tr_annotation_rows, f"{ANNOTATION}_report")
+    if tr_annotation_rows:
+        yield dlt.mark.with_table_name(tr_annotation_rows, f"{ANNOTATION}_report")
+
+    if error_reports:
+        yield dlt.mark.with_table_name(error_reports, "ncbi_import_error")
+
+
+@dlt.resource(name="assembly_list")
+def assembly_list(settings: NcbiSettings) -> Generator[list[str], Any, Any]:
+    """List of assemblies to fetch."""
+    batcher = BatchCursor(settings.input_dir, batch_size=1)
+    while files := batcher.get_batch():
+        for file_path in files:
+            with file_path.open() as f:
+                while next_chunk := list(islice(f, settings.batch_size)):
+                    yield [line.strip() for line in next_chunk if line.strip()]
+
+
+@dlt.transformer(name="assembly_reports", data_from=assembly_list, max_table_nesting=0, parallelized=True)
+def assembly_reports(
+    assembly_id_list: list[str],
+) -> Generator[dict[str, dict[str, dict[str, Any]] | list[dict[str, Any]]], Any]:
+    """Fetch reports for a list of assemblies from the NCBI datasets REST API."""
+    yield get_assembly_reports(assembly_id_list)
+
+
+@dlt.transformer(name="assembly_report_parser", data_from=assembly_reports, max_table_nesting=0, parallelized=True)
+def assembly_report_parser(
+    assembly_reports: dict[str, dict[str, Any]],
+) -> Generator[DataItemWithMeta, Any]:
+    """Parse and export assembly data from the REST API."""
+    return assemble_assembly_reports(assembly_reports)
 
 
-def run_ncbi_pipeline(config: Settings) -> None:
+def run_ncbi_pipeline(settings: NcbiSettings) -> None:
     """Run the NCBI datasets API pipeline.
 
-    :param config: configuration for the pipeline
-    :type config: Settings
+    :param settings: configuration for the pipeline
+    :type settings: NcbiSettings
     """
-    if config.dev_mode:
-        REST_CLIENT_HOOKS["response"] = [partial(save_raw_response, config)]
-    # update config according to the value of dev_mode
-    dlt.config["normalize.data_writer.disable_compression"] = config.dev_mode
+    if settings.dev_mode:
+        REST_CLIENT_HOOKS["response"] = [partial(save_raw_response, settings)]
 
-    # ensure that assembly_list has the correct config bound before running the pipeline
-    assembly_list.bind(config)
+    # ensure that assembly_list has the correct settings bound before running the pipeline
+    assembly_list.bind(settings)
 
     pipeline_kwargs = {
         "pipeline_name": DATASET_NAME,
         "dataset_name": DATASET_NAME,
-        "dev_mode": config.dev_mode,
     }
-    # set the output directory for all the pipeline gubbins
-    if config.use_output_dir_for_pipeline_metadata:
-        pipeline_kwargs["pipelines_dir"] = config.pipeline_dir
 
     run_pipeline(
-        config=config,
+        settings=settings,
         resource=[assembly_report_parser],
         destination_kwargs={"max_table_nesting": 0},
         pipeline_kwargs=pipeline_kwargs,
@@ -352,8 +321,8 @@ def run_ncbi_pipeline(config: Settings) -> None:
 
 
 def cli() -> None:
-    """CLI interface for the UniProt KB importer pipeline."""
-    run_cli(Settings, run_ncbi_pipeline)
+    """CLI interface for the NCBI REST API importer pipeline."""
+    run_cli(NcbiSettings, run_ncbi_pipeline)
 
 
 if __name__ == "__main__":
diff --git a/src/cdm_data_loaders/pipelines/uniprot_kb.py b/src/cdm_data_loaders/pipelines/uniprot_kb.py
index b6d1dc83..a17e5be1 100644
--- a/src/cdm_data_loaders/pipelines/uniprot_kb.py
+++ b/src/cdm_data_loaders/pipelines/uniprot_kb.py
@@ -13,39 +13,37 @@
     run_pipeline,
     stream_xml_file_resource,
 )
-from cdm_data_loaders.pipelines.cts_defaults import BatchedFileInputSettings
+from cdm_data_loaders.pipelines.cts_defaults import DEFAULT_SETTINGS_CONFIG_DICT, BatchedFileInputSettings
 
 APP_NAME = "uniprot_kb_importer"
 UNIPROT_LOG_INTERVAL = 1000
 
 
-class Settings(BatchedFileInputSettings):
+class UniProtSettings(BatchedFileInputSettings):
     """Configuration for running the UniProt KB import pipeline."""
 
     model_config = SettingsConfigDict(
-        cli_parse_args=True,
+        **DEFAULT_SETTINGS_CONFIG_DICT,
         cli_prog_name="uniprot",
-        cli_exit_on_error=False,
-        cli_ignore_unknown_args=True,
     )
 
 
 @dlt.resource(name="parse_uniprot", parallelized=True)
-def parse_uniprot(config: Settings) -> Generator[DataItemWithMeta, Any]:
+def parse_uniprot(settings: UniProtSettings) -> Generator[DataItemWithMeta, Any]:
     """Parse the information from UniProt files, batch by batch."""
     yield from stream_xml_file_resource(
-        config=config,
+        settings=settings,
         xml_tag=ENTRY_XML_TAG,
         parse_fn=parse_uniprot_entry,
         log_interval=UNIPROT_LOG_INTERVAL,
     )
 
 
-def run_uniprot_pipeline(config: Settings) -> None:
+def run_uniprot_pipeline(settings: UniProtSettings) -> None:
     """Execute the UniProt KB pipeline."""
     run_pipeline(
-        config=config,
-        resource=parse_uniprot(config),
+        settings=settings,
+        resource=parse_uniprot(settings),
         pipeline_kwargs={
             "pipeline_name": "uniprot_kb",
             "dataset_name": "uniprot_kb",
@@ -56,7 +54,7 @@ def run_uniprot_pipeline(config: Settings) -> None:
 
 def cli() -> None:
     """CLI interface for the UniProt KB importer pipeline."""
-    run_cli(Settings, run_uniprot_pipeline)
+    run_cli(UniProtSettings, run_uniprot_pipeline)
 
 
 if __name__ == "__main__":
diff --git a/src/cdm_data_loaders/pipelines/uniref.py b/src/cdm_data_loaders/pipelines/uniref.py
index 15bba8b3..f4703da5 100644
--- a/src/cdm_data_loaders/pipelines/uniref.py
+++ b/src/cdm_data_loaders/pipelines/uniref.py
@@ -15,28 +15,28 @@
     stream_xml_file_resource,
 )
 from cdm_data_loaders.pipelines.cts_defaults import (
+    DEFAULT_SETTINGS_CONFIG_DICT,
     BatchedFileInputSettings,
 )
-from cdm_data_loaders.utils.cdm_logger import get_cdm_logger
-
-logger = get_cdm_logger()
 
 APP_NAME = "uniref_importer"
 UNIREF_LOG_INTERVAL = 10000
 
 
-class Settings(BatchedFileInputSettings):
+UNIREF_VARIANT_ALIASES = ["-u", "--uniref", "--uniref-variant", "--uniref_variant"]
+
+
+class UnirefSettings(BatchedFileInputSettings):
     """Configuration for running the UniRef import pipeline."""
 
     model_config = SettingsConfigDict(
-        cli_parse_args=True,
+        **DEFAULT_SETTINGS_CONFIG_DICT,
         cli_prog_name="uniref",
-        cli_exit_on_error=False,
-        cli_ignore_unknown_args=True,
     )
+
     uniref_variant: str = Field(
         description=f"Which UniRef variant to import. Choices: {UNIREF_VARIANTS}",
-        validation_alias=AliasChoices("u", "uniref", "uniref-variant", "uniref_variant"),
+        validation_alias=AliasChoices(*[alias.strip("-") for alias in UNIREF_VARIANT_ALIASES]),
     )
 
     @field_validator("uniref_variant")
@@ -57,33 +57,33 @@ def validate_uniref_variant(cls, v: str) -> str:
 
 
 @dlt.resource(name="parse_uniref", parallelized=True)
-def parse_uniref(config: Settings) -> Generator[DataItemWithMeta, Any]:
+def parse_uniref(settings: UnirefSettings) -> Generator[DataItemWithMeta, Any]:
     """Parse the information from UniRef files, batch by batch.
 
-    :param config: config for running the pipeline.
-    :type config: Settings
+    :param settings: config for running the pipeline.
+    :type settings: UnirefSettings
     """
     yield from stream_xml_file_resource(
-        config=config,
+        settings=settings,
         xml_tag=ENTRY_XML_TAG,
         parse_fn=lambda entry, timestamp, file_path: parse_uniref_entry(
-            entry=entry, timestamp=timestamp, file_path=file_path, uniref_variant=f"UniRef {config.uniref_variant}"
+            entry=entry, timestamp=timestamp, file_path=file_path, uniref_variant=f"UniRef {settings.uniref_variant}"
         ),
         log_interval=UNIREF_LOG_INTERVAL,
     )
 
 
-def run_uniref_pipeline(config: Settings) -> None:
+def run_uniref_pipeline(settings: UnirefSettings) -> None:
     """Execute the Uniref pipeline.
 
-    :param config: config for running the pipeline.
-    :type config: Settings
+    :param settings: config for running the pipeline.
+    :type settings: UnirefSettings
     """
     run_pipeline(
-        config=config,
-        resource=parse_uniref(config),
+        settings=settings,
+        resource=parse_uniref(settings),
         pipeline_kwargs={
-            "pipeline_name": f"uniref_{config.uniref_variant}",
+            "pipeline_name": f"uniref_{settings.uniref_variant}",
             "dataset_name": "uniprot_kb",
         },
         pipeline_run_kwargs={"table_format": "delta"},
@@ -92,7 +92,7 @@ def run_uniref_pipeline(config: Settings) -> None:
 
 def cli() -> None:
     """CLI interface for the UniRef importer pipeline."""
-    run_cli(Settings, run_uniref_pipeline)
+    run_cli(UnirefSettings, run_uniref_pipeline)
 
 
 if __name__ == "__main__":
diff --git a/src/cdm_data_loaders/readers/dsv.py b/src/cdm_data_loaders/readers/dsv.py
index 04712bbd..bd74280a 100644
--- a/src/cdm_data_loaders/readers/dsv.py
+++ b/src/cdm_data_loaders/readers/dsv.py
@@ -6,7 +6,7 @@
 from pyspark.sql.types import StringType, StructField, StructType
 
 from cdm_data_loaders.core.constants import INVALID_DATA_FIELD_NAME
-from cdm_data_loaders.utils.cdm_logger import get_cdm_logger, log_and_die
+from cdm_data_loaders.utils.cdm_logger import get_cdm_logger
 
 # mapping of delimiters to format names (for logging)
 # spark defaults to separating on commas if nothing is specified
@@ -57,7 +57,9 @@ def read(
     :rtype: DataFrame
     """
     if not isinstance(schema_fields, list) or not all(isinstance(field, StructField) for field in schema_fields):
-        log_and_die("schema_fields must be specified as a list of StructFields", TypeError)
+        err_msg = "schema_fields must be specified as a list of StructFields"
+        logger.error(err_msg)
+        raise TypeError(err_msg)
 
     if not options:
         options = {}
@@ -69,8 +71,9 @@ def read(
     }
 
     if dsv_options["mode"] != PERMISSIVE:
-        msg = "The only permitted read mode is PERMISSIVE."
-        log_and_die(msg, ValueError)
+        err_msg = "The only permitted read mode is PERMISSIVE."
+        logger.error(err_msg)
+        raise ValueError(err_msg)
 
     format_name = get_format_name(options.get("delimiter", options.get("sep")))
 
diff --git a/src/cdm_data_loaders/utils/download/core.py b/src/cdm_data_loaders/utils/download/core.py
index 1a189f4b..cf788203 100644
--- a/src/cdm_data_loaders/utils/download/core.py
+++ b/src/cdm_data_loaders/utils/download/core.py
@@ -8,7 +8,7 @@
 
 import httpx
 
-from cdm_data_loaders.utils.cdm_logger import get_cdm_logger, log_and_die
+from cdm_data_loaders.utils.cdm_logger import get_cdm_logger
 
 logger: logging.Logger = get_cdm_logger()
 
@@ -60,7 +60,9 @@ def validate_args(
 
         # shake hashing algorithms require a length for the hexdigest => too much faff, error out
         if checksum_fn not in hashlib.algorithms_available or checksum_fn.startswith("shake"):
-            log_and_die(f"Hashing algorithm {checksum_fn} not supported.", ValueError)
+            err_msg = f"Hashing algorithm {checksum_fn} not supported."
+            logger.error(err_msg)
+            raise ValueError(err_msg)
 
         destination = Path(destination)
         destination.parent.mkdir(parents=True, exist_ok=True)
diff --git a/tests/cassettes/get_assembly_reports.yaml b/tests/cassettes/get_assembly_reports.yaml
deleted file mode 100644
index a90cd811..00000000
--- a/tests/cassettes/get_assembly_reports.yaml
+++ /dev/null
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-        (Baizongia pistaciae)"},{"name":"host","value":"Baizongia pistaciae"}],"status":{"status":"live","when":"2014-01-30T15:13:22.847"},"host":"Baizongia
-        pistaciae","strain":"Bp (Baizongia pistaciae)"}},"assembly_stats":{"total_number_of_chromosomes":2,"total_sequence_length":"618379","total_ungapped_length":"618379","number_of_contigs":2,"contig_n50":615980,"contig_l50":1,"number_of_scaffolds":2,"scaffold_n50":615980,"scaffold_l50":1,"number_of_component_sequences":2,"atgc_count":"618379","gc_count":"156707","gc_percent":25.5},"annotation_info":{"name":"GCF_000007725.1-RS_2025_02_20","provider":"NCBI
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+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partab\thttps://osf.io/download/699683f15ea4de93a87afcb0/\te8afaacb6d129993cec98ffcb5599b3b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partac\thttps://osf.io/download/699684114b33cc07aa656282/\te2664c7c60a95bc9eaff3e80b701206b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partad\thttps://osf.io/download/69968431d15ba99fc8505c9c/\taca8f3d35632b99f5b13cf06d2dfd202\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partae\thttps://osf.io/download/69968457084b03f8e17afaac/\t0db6aafa3edabd5b11da2f5da9d2494e\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaf\thttps://osf.io/download/69968476e7c282aa87655d74/\tea583ab653f355b018bcba69e58ae964\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partag\thttps://osf.io/download/6996849c4b33cc07aa65629e/\td72f9fa2b783b463b1821dde896e77f0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partah\thttps://osf.io/download/699684bc3cb4dc7857505a3d/\tccdf3bb28d9dc7c2081f471f17d7b473\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partai\thttps://osf.io/download/699684e13cb4dc7857505a51/\t64aa8775e3c2ded3b49038accdf47033\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaj\thttps://osf.io/download/69968501cac098a96c65614b/\t4e1cbf1823ca9a22f46b825050c5f9be\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partak\thttps://osf.io/download/699685263cb4dc7857505a7c/\tff59625000f2826eeb9affdddc88dd4b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partal\thttps://osf.io/download/69968547084b03f8e17afb33/\t0604b4ca35cbb412fbebb68864ba6358\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partam\thttps://osf.io/download/699685653cb4dc7857505aae/\t66998da3044bc9e62d1f44e82eb728e3\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partan\thttps://osf.io/download/6996858b5ea4de93a87afd26/\t528ce379c8598fbe9595e49aded59ec6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partao\thttps://osf.io/download/699685ab084b03f8e17afb5d/\t2f499343a159ff4ea3de1458e8176f84\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partap\thttps://osf.io/download/699685cb4bb9d437e37b0150/\tc05e084351581053eccb91e7f04df374\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaq\thttps://osf.io/download/699685efd15ba99fc8505d51/\t3e5da4e08f5684924f70a8f626c42110\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partar\thttps://osf.io/download/6996860ee7c282aa87655e11/\t7a0f45f999e5a15062a5b4073791882b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partas\thttps://osf.io/download/69968635b54ab125c27b0145/\tc1157a34d91833667274c1924fd69159\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partat\thttps://osf.io/download/69968654084b03f8e17afc76/\t2669ca59d6f3149a10fd4e1f2743e0e0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partau\thttps://osf.io/download/6996867a4b33cc07aa6563e8/\ta07d5de0900f807ff3aa7ab3f1ca6df4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partav\thttps://osf.io/download/6996869a3cb4dc7857505b3b/\taf1c36b35bb84b008e47dbced70708d4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaw\thttps://osf.io/download/699686be084b03f8e17afca7/\t23e36ec31239c9141877a7f3d65460fe\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partax\thttps://osf.io/download/699686dfe7c282aa87655eb5/\td7cfa43a6165bc2bfb3926fd0bcc0496\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partay\thttps://osf.io/download/699687053cb4dc7857505b6e/\t55ea86437890abcfec0f9ddffaf2ffc2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaz\thttps://osf.io/download/69968729052a9f16d25060f4/\t55b0568264ea76c6701e5ac77be12627\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partba\thttps://osf.io/download/6996874d3cb4dc7857505b95/\t9126c458ea81f0440fe5706a7786abfa\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbb\thttps://osf.io/download/6996876d4b33cc07aa656503/\tf17056e1858017da483af62fe87a3a07\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbc\thttps://osf.io/download/69968790e7c282aa87655fd3/\t7591d05e18c4055d1cde5506b204258b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbd\thttps://osf.io/download/699687b149c305221d505e45/\t887efe276d2d7477ec5faf93f4ccccdc\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbe\thttps://osf.io/download/699687d43cb4dc7857505bc8/\tb3a85ace89f659547b216ba5767478a6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbf\thttps://osf.io/download/699687f5e7c282aa87656009/\t5fc21e4b801fd11347564a352670c599\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbg\thttps://osf.io/download/69968817cac098a96c65634a/\tb157e976e1f119251ff57ea40b06c0c6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbh\thttps://osf.io/download/6996883ccac098a96c65636c/\ted618c3fb088b9118cfd5da517490bfc\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbi\thttps://osf.io/download/6996886acac098a96c656386/\t23860634162f7e11e1550ee44fc5386d\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbj\thttps://osf.io/download/699688b25ea4de93a87afe61/\tf53929f71fc908bbe96b7556608394b9\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbk\thttps://osf.io/download/699688df052a9f16d2506195/\t5f1064653435726ed845f6677c14499e\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbl\thttps://osf.io/download/699689015ea4de93a87afe66/\t0c017f7977526da59caf58775391a2fd\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbm\thttps://osf.io/download/69968929d359b2eb3e6562a4/\t42919ef5052d403c939afc50da07fcd6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbn\thttps://osf.io/download/69968950084b03f8e17afea1/\te3ac984e21a3028c53080d4dfae53c8a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbo\thttps://osf.io/download/69968971d15ba99fc8505f0c/\tb4dde831d7c4ff68f446d472d9511ee0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbp\thttps://osf.io/download/69968999d15ba99fc8505f20/\t7d69c251bfb195461c5e618b08c9e50a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbq\thttps://osf.io/download/699689c3d359b2eb3e6562d0/\tfa77043bb8585b538d9e0dd9361e7ee2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbr\thttps://osf.io/download/699689ea3cb4dc7857505d31/\te1328de97905b91412d2bf42ca9c3ac8\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbs\thttps://osf.io/download/69968a124bb9d437e37b0201/\t6d54ac0a726c3b327c5fcd04ea7f376a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbt\thttps://osf.io/download/69968a3a3cb4dc7857505d3e/\teffb608ea9ab459dadf286e54725f1c4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbu\thttps://osf.io/download/69968a5dd15ba99fc8505f46/\te0eabd64163fea4fabe0b76655c6ad73\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbv\thttps://osf.io/download/699cfaefbf4a163f18fef470/\td6981213bfbbf0ca836314d00c1b4cac\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbw\thttps://osf.io/download/699cfb521b6d2a2430ee2c87/\t1ded130146662a5676a88b6b4914ed59\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbx\thttps://osf.io/download/699cfba9487a2a88b2b7f2ef/\tf67b09ab562031ebc69eafbfab10036e\t886.1\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaa\thttps://osf.io/download/69965b2e805edf0ba87af9a9/\t9ba9ae5d05935d82f5b95e47adf81b13\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partab\thttps://osf.io/download/69965d6a870e55721a7afa72/\t57a02d2d7620ed98e35b3176ddc9c3e6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partac\thttps://osf.io/download/69965d9388b45aa5c2505a3b/\t4f90d6403cc0dfeaa02576d20433c077\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partad\thttps://osf.io/download/69965dbb88b45aa5c2505a42/\t647dd6213835e00bb6ebf44bf3b3a3ee\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partae\thttps://osf.io/download/69965e019be0fbd77c655d05/\t52b09b151a14231c6b1a475ddf38d376\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaf\thttps://osf.io/download/69965e40efc481514a505a1e/\t241b6d238bbf0c877db2294f0afbff38\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partag\thttps://osf.io/download/69965e869be0fbd77c655d24/\tb88033906c5ee750d7ac5b342e88e3fb\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partah\thttps://osf.io/download/69965ea79be0fbd77c655d48/\t024cfd0a31a6d767428a21fa05a40340\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partai\thttps://osf.io/download/69965ecd870e55721a7afae7/\t8154c6fb78880abd2329334115ee2b27\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaj\thttps://osf.io/download/69965ef2870e55721a7afaf2/\tde5bf6d09ee350373912c2ceed2f0704\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partak\thttps://osf.io/download/69965f19830a2f4bb5655d14/\t0e91965f3795641f7bb546964ac01ffe\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partal\thttps://osf.io/download/69965f3cefc481514a505a52/\td750f34c7469886f5e5e4090a7c22422\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partam\thttps://osf.io/download/69965f67830a2f4bb5655d3d/\tdacb0d533a76d586ec51073cff046d5a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partan\thttps://osf.io/download/69965f92805edf0ba87afae3/\t695d94cbc005e922d8c56f7fb1342dce\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partao\thttps://osf.io/download/69965fb3870e55721a7afb51/\t353f329899ea12182a1aac5f1f5467c4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partap\thttps://osf.io/download/69965fd288b45aa5c2505b09/\tc596e878bed03caab48e745691dc55d3\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaq\thttps://osf.io/download/69965ff6870e55721a7afbaa/\t95be991f14a826dcdeb1d1cba3f7245c\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partar\thttps://osf.io/download/69966016efc481514a505abe/\t36567f90ab426c77ca4e802a83e0b380\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partas\thttps://osf.io/download/6996603a8cb09d4f62655cd7/\t993e2db64c09e8a6f3566466279dfd66\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partat\thttps://osf.io/download/699659e7ce54ce25fd91ca2a/\t4cb2d86e2e8e58ba371af3a1f99ff10a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partau\thttps://osf.io/download/6996605f870e55721a7afbc2/\t070608086580a7cf82c3c61bf6d3ced1\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partav\thttps://osf.io/download/699659559be0fbd77c655bd8/\t667b41439ae0478575d3574cddb669b1\t306.26\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_AFDB_map_with_batches.tsv.gz\thttps://osf.io/download/kebs4/\tbeabc34b497ac5cc7a2d670791f225cf\t129.95\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partaa\thttps://osf.io/download/4fwsm/\t7237c1f91bac08245ac5445be046f4a2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partab\thttps://osf.io/download/69969c0801d3283b3d655f5f/\t64cab8af59c79a8d0552753fde5ecf3b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partac\thttps://osf.io/download/69969c1bd359b2eb3e6565a8/\t6c972a181e4f2e40fcf35de3a5624833\t445.19\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch001.tar.gz\thttps://osf.io/download/cu5v9/\te06bae944ad219bb3a34a1d0bd10f204\t3042.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch002.tar.gz\thttps://osf.io/download/69058c6973ae592cbcc184a8/\t6543237399dcbdac0d376a57fc0f5cb3\t3052.5\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch003.tar.gz\thttps://osf.io/download/69058d997fad6f1a7f96c052/\t5b4b288330dac4894f79a9345d817dae\t3002.38\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch004.tar.gz\thttps://osf.io/download/69058eca8eb59182b79c3c46/\tc76f43bf8575eb77f8fb52a05b527df3\t3023.76\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch005.tar.gz\thttps://osf.io/download/6905902774f58e050abe2ba2/\t10f574298f9323effb5f31f2c1fe71ea\t3009.77\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch006.tar.gz\thttps://osf.io/download/690591608d9a457800e03fa5/\tc40701a688f429c7c0e4e2a9b885f723\t3026.3\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch007.tar.gz\thttps://osf.io/download/690592a318084463ae9c3638/\t595c49a83b388c31ef830b237a34f362\t3069.08\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch008.tar.gz\thttps://osf.io/download/690593dcbea989b1ebe0471e/\tb6b4cc688e94247fc2c0436948fe7c82\t3048.9\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch009.tar.gz\thttps://osf.io/download/6905951774f58e050abe2ebc/\t37dbb95b9ea56b40fd9582e099dcfae7\t3057.28\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch010.tar.gz\thttps://osf.io/download/6905964c3ca2b133ea9c3362/\tdff0da05b2d648273be737565aac38fa\t3044.09\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch011.tar.gz\thttps://osf.io/download/6905977e7fad6f1a7f96c6ad/\t953d4babb6be525a08f3a9054de05717\t3034.63\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch012.tar.gz\thttps://osf.io/download/690598b018084463ae9c3a1b/\t9e684775c9a65332183dfa07c8bb4fe7\t3017.61\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch013.tar.gz\thttps://osf.io/download/690599e18d6eecf23596c2f6/\t592d68c574d21084f82bb85f1e3bd93e\t3011.41\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch014.tar.gz\thttps://osf.io/download/69059b136547f95044c18107/\tb4e0a7e9bc06c880a6cbc4b6aaded8e1\t3033.59\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch015.tar.gz\thttps://osf.io/download/69059c4f262158bef5e03c08/\t6a3c8e53f286f2e28f1ec6ffde7a67c8\t3022.08\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch016.tar.gz\thttps://osf.io/download/69059d88a4e3803073e04313/\tc543ec9ebe43cbc189ef03a1ff7b0d38\t3037.36\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch024.tar.gz\thttps://osf.io/download/68fefbd1faa7701248c400ba/\tede17e4d7b55ac9ea063afb70570ea03\t3043.79\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch028.tar.gz\thttps://osf.io/download/68ff00f25eeff9e71c19ff00/\t77aa5f8fe70717fd97cbf67558d787f0\t3039.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set2\tjn4ah\tbatch029.tar.gz\thttps://osf.io/download/68ff0223627c5ce7b6c3ffe3/\t069e649606a603322349dd30a8777743\t3012.98\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch031.tar.gz\thttps://osf.io/download/68ff0487f783a417f4f98322/\t49a9de5003924533e3b22276a759711f\t3002.31\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set3\thxsyj\tbatch033.tar.gz\thttps://osf.io/download/68ff1049f650be1ea6497136/\t0cd076edae66be4d253b6687b9144936\t3045.85\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch034.tar.gz\thttps://osf.io/download/68ff1179e4a4cb6427f97da4/\t2c61e16701ca9f23b478170c86038630\t3020.56\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch035.tar.gz\thttps://osf.io/download/68ff12ac6d3db72b9119fd07/\t66e4c9bf805637c25d4156b64193f621\t3039.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch036.tar.gz\thttps://osf.io/download/68ff13f45eeff9e71c1a01b9/\tca9899473fb2ca00acad2b9cb7c859bb\t3048.62\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch037.tar.gz\thttps://osf.io/download/68ff1526a7953cbb6df981ba/\t48aa802f6315d441e79e9a7c6fe3c8c8\t3018.38\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch038.tar.gz\thttps://osf.io/download/68ff166103ef1d4af37f28c7/\t68cdf8dffee5cb922031ea2f5f5b252d\t3071.25\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch039.tar.gz\thttps://osf.io/download/68ff1797a46afc65fbf97e41/\t5cfff7ab84aa3a2a5aa4d2cb439f91ad\t3054.98\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch040.tar.gz\thttps://osf.io/download/68ff18d36d3db72b9119fe24/\t5488080a09ab5bcf28accc869bdd1ed9\t3071.86\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch041.tar.gz\thttps://osf.io/download/68ff1a0503c857b42319ff2f/\t258cb681ee06a5804124b5123f33e713\t3041.61\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch042.tar.gz\thttps://osf.io/download/68ff1b3e92dfa08278c3ff78/\t9b8b8a22ec7279687185f1c36b31c452\t3063.64\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch043.tar.gz\thttps://osf.io/download/68ff1c736d3db72b9119feed/\t33f0cd8fc51907e2afca9ac151c2b22c\t3056.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch044.tar.gz\thttps://osf.io/download/68ff1da8a46afc65fbf97f6b/\tfe205155fe0bb4ddb13a9ec38377f766\t3054.96\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch045.tar.gz\thttps://osf.io/download/68ff1ed8be609d3b68c401b4/\t656bd92157725fde63b39866829f8d29\t3027.45\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch046.tar.gz\thttps://osf.io/download/68ff200ce4a4cb6427f981c0/\ted9da7c3941abb2e9577bb31f1517f54\t3037.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch047.tar.gz\thttps://osf.io/download/68ff217699935977d04970b5/\t82c5acc860a97449eb9ab40a4acaa8c0\t3009.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch048.tar.gz\thttps://osf.io/download/68ff4e1ca743ab1938c3ffff/\te92a33c99c737b29ee5a0be50a3c1ecf\t3062.12\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch049.tar.gz\thttps://osf.io/download/68ff4b87680d8dd9f6f985a8/\t9a328ee6a256407737654c71ba3a83f7\t3055.21\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch050.tar.gz\thttps://osf.io/download/68ff509c9d683136574978a1/\t8d6ebfa8989247ae39c5d5b7b43c74d8\t3065.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch051.tar.gz\thttps://osf.io/download/68ff50538e2dab3f9119fdfd/\t6bdd28681fdd01797f67536da2ff5ce6\t3037.36\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch052.tar.gz\thttps://osf.io/download/68ff51871e852f3868f986f6/\t3920eb418a2e79495c412d8811b2a7a1\t3005.94\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch053.tar.gz\thttps://osf.io/download/68ff52bdcebefe2c2ef9845e/\t15cc752786ca6b7d3db26774a04fd87f\t3033.81\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch054.tar.gz\thttps://osf.io/download/68ff593667b36546b9f97f3e/\t5eeec63e3ae3fb5847d3fe0c4a4d3cd3\t3036.89\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch055.tar.gz\thttps://osf.io/download/68ff5c401ca7a2551819fc4b/\tcef9a8378baa10a508d83f41d40b05aa\t2988.85\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch056.tar.gz\thttps://osf.io/download/68ff5d357fd038907149707b/\t7ae6465d56769bb3078a315ae7bfd3ad\t3085.43\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch057.tar.gz\thttps://osf.io/download/68ff5e766a384dd8c77f2cb7/\t68551f09782ca6fd2d3c223d8a388972\t3052.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch058.tar.gz\thttps://osf.io/download/68ff5fad6a384dd8c77f2d6f/\t8e27f162b3a92440aa8a5147af3e3120\t3018.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch059.tar.gz\thttps://osf.io/download/68ff60e28fdd670e2a7f2d73/\t0e2e36d2b0c45b49f57481a58214afaf\t3007.99\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch060.tar.gz\thttps://osf.io/download/68ff621a5b66297f96f98217/\tf1429d433777c35dbb5da6b8f90a3eca\t3074.55\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch061.tar.gz\thttps://osf.io/download/68ff63570983ff67d7c4056d/\t0d606bfe794ecf59d14255af295e0a8e\t3082.74\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch062.tar.gz\thttps://osf.io/download/68ff648f8f37a9090a19ff7a/\t0e0e5725ee405a23bffff61e6aa65172\t3069.78\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch063.tar.gz\thttps://osf.io/download/68ff65c881df3ad7c7f97e46/\ted0631dd388e5ba23598c97b4242338c\t3055.15\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch064.tar.gz\thttps://osf.io/download/68fffdb1fcb9bdb879497022/\tdcb5b4ef49c29178c5f58a453cf56db9\t3060.03\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch065.tar.gz\thttps://osf.io/download/68fffef5b4986ff6c7f9817f/\t161cddb9e2f3e0140af4b910c6aec62f\t3028.48\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch066.tar.gz\thttps://osf.io/download/69000025e5dc081a9f497220/\tead350c4844487beaa7ac4ba561dd084\t2983.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch067.tar.gz\thttps://osf.io/download/69000159dd94b2d9307f3200/\t59afa546f7c7a77fe9cf5faf7579b001\t3035.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch068.tar.gz\thttps://osf.io/download/6900028f0dbc782bd4c40204/\t07a32e31c80c6a0cf2a36a33f5e39dc8\t3065.68\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch069.tar.gz\thttps://osf.io/download/690003c7fcb9bdb879497833/\t43aadf6c44889549e9f9623f46a19e27\t3044.12\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch070.tar.gz\thttps://osf.io/download/690004f99805973b6a7f2ad5/\tf6a3e4fb6f25c7988d5b00aa926adfde\t3024.71\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch071.tar.gz\thttps://osf.io/download/690006329805973b6a7f2b3e/\t0bdbb21eb141bc95d47145d384047cbd\t3057.43\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch072.tar.gz\thttps://osf.io/download/69000767fcb9bdb87949795b/\t2ce68c4d57e4dd2d1f195e033857a5fa\t3035.59\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch073.tar.gz\thttps://osf.io/download/690008985b0fb1153a7f3239/\tea21b3d51a5890e86e2a9f2575d2ce53\t2983.82\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch074.tar.gz\thttps://osf.io/download/690009d44d27537968f9839b/\td65bcac016ed3ef3278a7ea6b084ce7f\t3069.8\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch075.tar.gz\thttps://osf.io/download/69000b0cece1b4c4cdf986e6/\t98b26950520aa178ebec4862d43a71b3\t3032.39\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch076.tar.gz\thttps://osf.io/download/69000c3f50c67e23381a0186/\te647c2c22722cbc85ad2ba1347f6d79f\t3011.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch077.tar.gz\thttps://osf.io/download/69000d760dbc782bd4c407d7/\td2e8fcd726d4be99fd030939c747d41b\t3048.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch078.tar.gz\thttps://osf.io/download/69000ea89805973b6a7f2dba/\t45414dc9145f276987410bf65ec8dd08\t3012.4\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch079.tar.gz\thttps://osf.io/download/69000fdc5b0fb1153a7f338a/\tbe66d3fe6415ea5b1124a28413aaab79\t3010.96\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch080.tar.gz\thttps://osf.io/download/69002e1933087ee35fc40689/\t019a4ef2f4f2b17a2b922bdb759e620c\t3074.39\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch081.tar.gz\thttps://osf.io/download/69002f4c77533fb55af984dd/\tb8fc1b7268c521f4ce8c981d4761ebf7\t3050.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch082.tar.gz\thttps://osf.io/download/6900307efe5543131949722d/\tc81d788151bd64fd773b63b9ce78a909\t3006.79\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch083.tar.gz\thttps://osf.io/download/690031b6afea32ad157f2c0e/\teb70eddd2de48056fae0e4e335a58581\t3068.07\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch084.tar.gz\thttps://osf.io/download/690032e3e9177e17fe4975b5/\tc6a4351ad256b3053650224866315510\t2995.82\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch085.tar.gz\thttps://osf.io/download/69003419fe554313194972d6/\tb515b1a1409780f7f5499cf7500da014\t3033.98\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch086.tar.gz\thttps://osf.io/download/690035546d0bea46b0f98284/\tc8e14503d9be0dcf13cb0f0c80a66851\t3094.99\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch087.tar.gz\thttps://osf.io/download/690036865ece85c294c40379/\t97df34cc486087e43b6d12aa587d8ccc\t3033.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch088.tar.gz\thttps://osf.io/download/690037b71aea2afeac7f32b6/\tdf3a9886bb69fd187b8fbd2c15336fb0\t3022.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch089.tar.gz\thttps://osf.io/download/690038f1a745ae8daf7f27d0/\t90944d95178b5a3401e3b2c05c5ef0a5\t3116.02\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch090.tar.gz\thttps://osf.io/download/69003a285ece85c294c40523/\t37a0f9a48a4ba77c30c7347fd7166fe6\t3076.5\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch091.tar.gz\thttps://osf.io/download/69003b5ae12b5f7e55c3fc8a/\ta281ec2388226d0ada9f32e1a34b85bd\t3018.18\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set6\tybs2x\tbatch093.tar.gz\thttps://osf.io/download/69003dce6d0bea46b0f98456/\t94190534d49ff88064f47306d586729d\t3075.01\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch094.tar.gz\thttps://osf.io/download/69003efe4241085c1b4977d4/\t8ca221c914d63b27776aa0d5b668b007\t3009.6\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch095.tar.gz\thttps://osf.io/download/6900402ee02f38aecd49703c/\t32ace265f198c9ce48e95cecd5e3f33d\t3007.13\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set7\t3ns7e\tbatch097.tar.gz\thttps://osf.io/download/69004e3078f346092319fc71/\tae3e082ce7307feebd9e591c147318eb\t3057.86\nAllTheBacteria/Hypothetical
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046e1/\t9174e37497674641d9b22d2df90d8194\t43.28\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.663.cobs_classic.xz\thttps://osf.io/download/666c39240f8c8014543c948f/\te35d4f8c3adb48c8d54141e119817417\t19.22\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.664.cobs_classic.xz\thttps://osf.io/download/666c394c6b6c8e309404cf8e/\t31ce112d43bb5e65ca3c6ab79eb8b265\t177.33\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.665.cobs_classic.xz\thttps://osf.io/download/666c393965e1de5abb893df0/\t4a43e0ba59653fd25097749ace019722\t63.51\nAllTheBacteria/Indexes/sketchlib\trceq5\t0.2/atb_sketchlib_v020.skd\thttps://osf.io/download/usrcx/\t6117b38379c853f8b11f430ce2da7f99\t3303.15\nAllTheBacteria/Indexes/sketchlib\trceq5\t0.2/atb_sketchlib_v020.skm\thttps://osf.io/download/etjyu/\t422404b643d3ed7cf99b199371a410d7\t96.53\nAllTheBacteria/Indexes/sketchlib\trceq5\tAggregated/atb_sketchlib.aggregated.202408.skd\thttps://osf.io/download/92qmr/\t8c795bef62e5814e44387d5e912982ca\t4170.57\nAllTheBacteria/Indexes/sketchlib\trceq5\tAggregated/atb_sketchlib.aggregated.202408.skm\thttps://osf.io/download/nwfkc/\ta743351fe92efd8bab2df4209779e125\t122.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.103.tar.gz\thttps://osf.io/download/69951ac4f271898ad8506110/\t667b44afd96e6a40cc14dcaa903a089f\t770.72\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.104.tar.gz\thttps://osf.io/download/69951adf52855323c26caf88/\t6783bdb1a3a79a279d3925bf1f68add9\t832.44\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.105.tar.gz\thttps://osf.io/download/69951af8718b42a0936cacc5/\t1e73749ce0a449b97a4a096146cf41d8\t868.93\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.107.tar.gz\thttps://osf.io/download/69951a57d60c1a9ed3505f39/\t000104e5dba8e4032bcaca1a74d8127c\t557.52\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.108.tar.gz\thttps://osf.io/download/69951a93e425a51c05fa3bf7/\t00d9d1f7662396cb966cfa2cbf26ec88\t658.07\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.111.tar.gz\thttps://osf.io/download/69951a20d60c1a9ed3505f37/\t61da5eba73e7486a3f6a9890ef485bad\t437.96\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.130.tar.gz\thttps://osf.io/download/69951a0f7c6af22d0bfa427a/\tbb8f5ff7c2ab6360efa21e100d555bab\t186.55\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.139.tar.gz\thttps://osf.io/download/69951aa87d93b6b5866ca814/\t2d2fa6074a78bcea9fc930701af8c73d\t688.06\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.140.tar.gz\thttps://osf.io/download/69951bb846ad0a518d6caf2d/\t7dd0eb6f179d9d21298ff0a95659ac00\t1243.3\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-aa\thttps://osf.io/download/6993e501f3f21e18a2594315/\t2540c9029cbc9741c6e3a8479db42e95\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ab\thttps://osf.io/download/6993e5d2a2d0eb28e0c36346/\te306e01fb9ab285b92e089c37f68eb53\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ac\thttps://osf.io/download/6993e64492d922d571d16802/\t9337c023b8dc36b468d633e636fd4447\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ad\thttps://osf.io/download/6993e42d795c00d55a594166/\td40823125ed566c5763cd7f7108e2c66\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ae\thttps://osf.io/download/6993e51b795c00d55a59421b/\t7ff8c8a614adaf40eccf92c767ed5b0e\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-af\thttps://osf.io/download/6993e5cbb8a39504f3c363b5/\t89a4d83ae3b3d835b4a4ce717b4542e9\t3703.99\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.15.tar.gz\thttps://osf.io/download/69951a45451c19d54b505c62/\t100906ef7809b897c71393f9a900d0e9\t509.88\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.17.tar.gz\thttps://osf.io/download/69951a30f271898ad85060e3/\t61133acde6203e6dd2244699523911c6\t453.42\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.192.tar.gz\thttps://osf.io/download/6993dc9ca2d0eb28e0c36006/\t9587aa9ebb9f1b8d00adbe047a9ec4e1\t1016.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.197.tar.gz\thttps://osf.io/download/69951b37d60c1a9ed3505f4e/\ta5057dd9f9e2c31f9e5847d2338cda44\t1150.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.210.tar.gz\thttps://osf.io/download/69951a69451c19d54b505c6b/\tf7c0c616f59fec798c2328c94d96efd3\t570.8\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.30.tar.gz\thttps://osf.io/download/3pmqt/\t802f44abaf6b954ca051f6470a2b5282\t594.06\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.r0.2.batch.138.tar.gz\thttps://osf.io/download/69951b7b718b42a0936cacd9/\tf737d5c0ccc68e97d66df7c28801251f\t1216.78\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.r0.2.batch.150.tar.gz\thttps://osf.io/download/69951b18718b42a0936cacce/\t3363a588874a0a800b78f7fbf8a579d2\t994.22\nAllTheBacteria/MGE
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+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partab\thttps://osf.io/download/699683f15ea4de93a87afcb0/\te8afaacb6d129993cec98ffcb5599b3b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partac\thttps://osf.io/download/699684114b33cc07aa656282/\te2664c7c60a95bc9eaff3e80b701206b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partad\thttps://osf.io/download/69968431d15ba99fc8505c9c/\taca8f3d35632b99f5b13cf06d2dfd202\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partae\thttps://osf.io/download/69968457084b03f8e17afaac/\t0db6aafa3edabd5b11da2f5da9d2494e\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaf\thttps://osf.io/download/69968476e7c282aa87655d74/\tea583ab653f355b018bcba69e58ae964\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partag\thttps://osf.io/download/6996849c4b33cc07aa65629e/\td72f9fa2b783b463b1821dde896e77f0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partah\thttps://osf.io/download/699684bc3cb4dc7857505a3d/\tccdf3bb28d9dc7c2081f471f17d7b473\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partai\thttps://osf.io/download/699684e13cb4dc7857505a51/\t64aa8775e3c2ded3b49038accdf47033\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaj\thttps://osf.io/download/69968501cac098a96c65614b/\t4e1cbf1823ca9a22f46b825050c5f9be\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partak\thttps://osf.io/download/699685263cb4dc7857505a7c/\tff59625000f2826eeb9affdddc88dd4b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partal\thttps://osf.io/download/69968547084b03f8e17afb33/\t0604b4ca35cbb412fbebb68864ba6358\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partam\thttps://osf.io/download/699685653cb4dc7857505aae/\t66998da3044bc9e62d1f44e82eb728e3\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partan\thttps://osf.io/download/6996858b5ea4de93a87afd26/\t528ce379c8598fbe9595e49aded59ec6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partao\thttps://osf.io/download/699685ab084b03f8e17afb5d/\t2f499343a159ff4ea3de1458e8176f84\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partap\thttps://osf.io/download/699685cb4bb9d437e37b0150/\tc05e084351581053eccb91e7f04df374\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaq\thttps://osf.io/download/699685efd15ba99fc8505d51/\t3e5da4e08f5684924f70a8f626c42110\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partar\thttps://osf.io/download/6996860ee7c282aa87655e11/\t7a0f45f999e5a15062a5b4073791882b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partas\thttps://osf.io/download/69968635b54ab125c27b0145/\tc1157a34d91833667274c1924fd69159\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partat\thttps://osf.io/download/69968654084b03f8e17afc76/\t2669ca59d6f3149a10fd4e1f2743e0e0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partau\thttps://osf.io/download/6996867a4b33cc07aa6563e8/\ta07d5de0900f807ff3aa7ab3f1ca6df4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partav\thttps://osf.io/download/6996869a3cb4dc7857505b3b/\taf1c36b35bb84b008e47dbced70708d4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaw\thttps://osf.io/download/699686be084b03f8e17afca7/\t23e36ec31239c9141877a7f3d65460fe\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partax\thttps://osf.io/download/699686dfe7c282aa87655eb5/\td7cfa43a6165bc2bfb3926fd0bcc0496\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partay\thttps://osf.io/download/699687053cb4dc7857505b6e/\t55ea86437890abcfec0f9ddffaf2ffc2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partaz\thttps://osf.io/download/69968729052a9f16d25060f4/\t55b0568264ea76c6701e5ac77be12627\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partba\thttps://osf.io/download/6996874d3cb4dc7857505b95/\t9126c458ea81f0440fe5706a7786abfa\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbb\thttps://osf.io/download/6996876d4b33cc07aa656503/\tf17056e1858017da483af62fe87a3a07\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbc\thttps://osf.io/download/69968790e7c282aa87655fd3/\t7591d05e18c4055d1cde5506b204258b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbd\thttps://osf.io/download/699687b149c305221d505e45/\t887efe276d2d7477ec5faf93f4ccccdc\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbe\thttps://osf.io/download/699687d43cb4dc7857505bc8/\tb3a85ace89f659547b216ba5767478a6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbf\thttps://osf.io/download/699687f5e7c282aa87656009/\t5fc21e4b801fd11347564a352670c599\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbg\thttps://osf.io/download/69968817cac098a96c65634a/\tb157e976e1f119251ff57ea40b06c0c6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbh\thttps://osf.io/download/6996883ccac098a96c65636c/\ted618c3fb088b9118cfd5da517490bfc\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbi\thttps://osf.io/download/6996886acac098a96c656386/\t23860634162f7e11e1550ee44fc5386d\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbj\thttps://osf.io/download/699688b25ea4de93a87afe61/\tf53929f71fc908bbe96b7556608394b9\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbk\thttps://osf.io/download/699688df052a9f16d2506195/\t5f1064653435726ed845f6677c14499e\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbl\thttps://osf.io/download/699689015ea4de93a87afe66/\t0c017f7977526da59caf58775391a2fd\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbm\thttps://osf.io/download/69968929d359b2eb3e6562a4/\t42919ef5052d403c939afc50da07fcd6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbn\thttps://osf.io/download/69968950084b03f8e17afea1/\te3ac984e21a3028c53080d4dfae53c8a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbo\thttps://osf.io/download/69968971d15ba99fc8505f0c/\tb4dde831d7c4ff68f446d472d9511ee0\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbp\thttps://osf.io/download/69968999d15ba99fc8505f20/\t7d69c251bfb195461c5e618b08c9e50a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbq\thttps://osf.io/download/699689c3d359b2eb3e6562d0/\tfa77043bb8585b538d9e0dd9361e7ee2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbr\thttps://osf.io/download/699689ea3cb4dc7857505d31/\te1328de97905b91412d2bf42ca9c3ac8\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbs\thttps://osf.io/download/69968a124bb9d437e37b0201/\t6d54ac0a726c3b327c5fcd04ea7f376a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbt\thttps://osf.io/download/69968a3a3cb4dc7857505d3e/\teffb608ea9ab459dadf286e54725f1c4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases\twpyeh\tfoldcomp_db.tar.gz_partbu\thttps://osf.io/download/69968a5dd15ba99fc8505f46/\te0eabd64163fea4fabe0b76655c6ad73\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbv\thttps://osf.io/download/699cfaefbf4a163f18fef470/\td6981213bfbbf0ca836314d00c1b4cac\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbw\thttps://osf.io/download/699cfb521b6d2a2430ee2c87/\t1ded130146662a5676a88b6b4914ed59\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2\tf3edq\tfoldcomp_db.tar.gz_partbx\thttps://osf.io/download/699cfba9487a2a88b2b7f2ef/\tf67b09ab562031ebc69eafbfab10036e\t886.1\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaa\thttps://osf.io/download/69965b2e805edf0ba87af9a9/\t9ba9ae5d05935d82f5b95e47adf81b13\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partab\thttps://osf.io/download/69965d6a870e55721a7afa72/\t57a02d2d7620ed98e35b3176ddc9c3e6\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partac\thttps://osf.io/download/69965d9388b45aa5c2505a3b/\t4f90d6403cc0dfeaa02576d20433c077\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partad\thttps://osf.io/download/69965dbb88b45aa5c2505a42/\t647dd6213835e00bb6ebf44bf3b3a3ee\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partae\thttps://osf.io/download/69965e019be0fbd77c655d05/\t52b09b151a14231c6b1a475ddf38d376\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaf\thttps://osf.io/download/69965e40efc481514a505a1e/\t241b6d238bbf0c877db2294f0afbff38\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partag\thttps://osf.io/download/69965e869be0fbd77c655d24/\tb88033906c5ee750d7ac5b342e88e3fb\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partah\thttps://osf.io/download/69965ea79be0fbd77c655d48/\t024cfd0a31a6d767428a21fa05a40340\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partai\thttps://osf.io/download/69965ecd870e55721a7afae7/\t8154c6fb78880abd2329334115ee2b27\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaj\thttps://osf.io/download/69965ef2870e55721a7afaf2/\tde5bf6d09ee350373912c2ceed2f0704\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partak\thttps://osf.io/download/69965f19830a2f4bb5655d14/\t0e91965f3795641f7bb546964ac01ffe\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partal\thttps://osf.io/download/69965f3cefc481514a505a52/\td750f34c7469886f5e5e4090a7c22422\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partam\thttps://osf.io/download/69965f67830a2f4bb5655d3d/\tdacb0d533a76d586ec51073cff046d5a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partan\thttps://osf.io/download/69965f92805edf0ba87afae3/\t695d94cbc005e922d8c56f7fb1342dce\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partao\thttps://osf.io/download/69965fb3870e55721a7afb51/\t353f329899ea12182a1aac5f1f5467c4\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partap\thttps://osf.io/download/69965fd288b45aa5c2505b09/\tc596e878bed03caab48e745691dc55d3\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partaq\thttps://osf.io/download/69965ff6870e55721a7afbaa/\t95be991f14a826dcdeb1d1cba3f7245c\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partar\thttps://osf.io/download/69966016efc481514a505abe/\t36567f90ab426c77ca4e802a83e0b380\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partas\thttps://osf.io/download/6996603a8cb09d4f62655cd7/\t993e2db64c09e8a6f3566466279dfd66\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partat\thttps://osf.io/download/699659e7ce54ce25fd91ca2a/\t4cb2d86e2e8e58ba371af3a1f99ff10a\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partau\thttps://osf.io/download/6996605f870e55721a7afbc2/\t070608086580a7cf82c3c61bf6d3ced1\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Foldseek_Databases\tfr37t\tfoldseek_db.tar.gz_partav\thttps://osf.io/download/699659559be0fbd77c655bd8/\t667b41439ae0478575d3574cddb669b1\t306.26\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_AFDB_map_with_batches.tsv.gz\thttps://osf.io/download/kebs4/\tbeabc34b497ac5cc7a2d670791f225cf\t129.95\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partaa\thttps://osf.io/download/4fwsm/\t7237c1f91bac08245ac5445be046f4a2\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partab\thttps://osf.io/download/69969c0801d3283b3d655f5f/\t64cab8af59c79a8d0552753fde5ecf3b\t1024.0\nAllTheBacteria/Hypothetical
+        Protein Structures/Metadata\t3qrey\tATB_every_protein_with_species.tsv.gz_partac\thttps://osf.io/download/69969c1bd359b2eb3e6565a8/\t6c972a181e4f2e40fcf35de3a5624833\t445.19\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch001.tar.gz\thttps://osf.io/download/cu5v9/\te06bae944ad219bb3a34a1d0bd10f204\t3042.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch002.tar.gz\thttps://osf.io/download/69058c6973ae592cbcc184a8/\t6543237399dcbdac0d376a57fc0f5cb3\t3052.5\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch003.tar.gz\thttps://osf.io/download/69058d997fad6f1a7f96c052/\t5b4b288330dac4894f79a9345d817dae\t3002.38\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch004.tar.gz\thttps://osf.io/download/69058eca8eb59182b79c3c46/\tc76f43bf8575eb77f8fb52a05b527df3\t3023.76\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch005.tar.gz\thttps://osf.io/download/6905902774f58e050abe2ba2/\t10f574298f9323effb5f31f2c1fe71ea\t3009.77\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch006.tar.gz\thttps://osf.io/download/690591608d9a457800e03fa5/\tc40701a688f429c7c0e4e2a9b885f723\t3026.3\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch007.tar.gz\thttps://osf.io/download/690592a318084463ae9c3638/\t595c49a83b388c31ef830b237a34f362\t3069.08\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch008.tar.gz\thttps://osf.io/download/690593dcbea989b1ebe0471e/\tb6b4cc688e94247fc2c0436948fe7c82\t3048.9\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch009.tar.gz\thttps://osf.io/download/6905951774f58e050abe2ebc/\t37dbb95b9ea56b40fd9582e099dcfae7\t3057.28\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch010.tar.gz\thttps://osf.io/download/6905964c3ca2b133ea9c3362/\tdff0da05b2d648273be737565aac38fa\t3044.09\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch011.tar.gz\thttps://osf.io/download/6905977e7fad6f1a7f96c6ad/\t953d4babb6be525a08f3a9054de05717\t3034.63\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch012.tar.gz\thttps://osf.io/download/690598b018084463ae9c3a1b/\t9e684775c9a65332183dfa07c8bb4fe7\t3017.61\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch013.tar.gz\thttps://osf.io/download/690599e18d6eecf23596c2f6/\t592d68c574d21084f82bb85f1e3bd93e\t3011.41\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch014.tar.gz\thttps://osf.io/download/69059b136547f95044c18107/\tb4e0a7e9bc06c880a6cbc4b6aaded8e1\t3033.59\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch015.tar.gz\thttps://osf.io/download/69059c4f262158bef5e03c08/\t6a3c8e53f286f2e28f1ec6ffde7a67c8\t3022.08\nAllTheBacteria/Hypothetical
+        Protein Structures/Set1\tsw6p8\tbatch016.tar.gz\thttps://osf.io/download/69059d88a4e3803073e04313/\tc543ec9ebe43cbc189ef03a1ff7b0d38\t3037.36\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch024.tar.gz\thttps://osf.io/download/68fefbd1faa7701248c400ba/\tede17e4d7b55ac9ea063afb70570ea03\t3043.79\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch028.tar.gz\thttps://osf.io/download/68ff00f25eeff9e71c19ff00/\t77aa5f8fe70717fd97cbf67558d787f0\t3039.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set2\tjn4ah\tbatch029.tar.gz\thttps://osf.io/download/68ff0223627c5ce7b6c3ffe3/\t069e649606a603322349dd30a8777743\t3012.98\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set2\tjn4ah\tbatch031.tar.gz\thttps://osf.io/download/68ff0487f783a417f4f98322/\t49a9de5003924533e3b22276a759711f\t3002.31\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set3\thxsyj\tbatch033.tar.gz\thttps://osf.io/download/68ff1049f650be1ea6497136/\t0cd076edae66be4d253b6687b9144936\t3045.85\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch034.tar.gz\thttps://osf.io/download/68ff1179e4a4cb6427f97da4/\t2c61e16701ca9f23b478170c86038630\t3020.56\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch035.tar.gz\thttps://osf.io/download/68ff12ac6d3db72b9119fd07/\t66e4c9bf805637c25d4156b64193f621\t3039.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch036.tar.gz\thttps://osf.io/download/68ff13f45eeff9e71c1a01b9/\tca9899473fb2ca00acad2b9cb7c859bb\t3048.62\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch037.tar.gz\thttps://osf.io/download/68ff1526a7953cbb6df981ba/\t48aa802f6315d441e79e9a7c6fe3c8c8\t3018.38\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch038.tar.gz\thttps://osf.io/download/68ff166103ef1d4af37f28c7/\t68cdf8dffee5cb922031ea2f5f5b252d\t3071.25\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch039.tar.gz\thttps://osf.io/download/68ff1797a46afc65fbf97e41/\t5cfff7ab84aa3a2a5aa4d2cb439f91ad\t3054.98\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch040.tar.gz\thttps://osf.io/download/68ff18d36d3db72b9119fe24/\t5488080a09ab5bcf28accc869bdd1ed9\t3071.86\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch041.tar.gz\thttps://osf.io/download/68ff1a0503c857b42319ff2f/\t258cb681ee06a5804124b5123f33e713\t3041.61\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch042.tar.gz\thttps://osf.io/download/68ff1b3e92dfa08278c3ff78/\t9b8b8a22ec7279687185f1c36b31c452\t3063.64\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch043.tar.gz\thttps://osf.io/download/68ff1c736d3db72b9119feed/\t33f0cd8fc51907e2afca9ac151c2b22c\t3056.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch044.tar.gz\thttps://osf.io/download/68ff1da8a46afc65fbf97f6b/\tfe205155fe0bb4ddb13a9ec38377f766\t3054.96\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch045.tar.gz\thttps://osf.io/download/68ff1ed8be609d3b68c401b4/\t656bd92157725fde63b39866829f8d29\t3027.45\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch046.tar.gz\thttps://osf.io/download/68ff200ce4a4cb6427f981c0/\ted9da7c3941abb2e9577bb31f1517f54\t3037.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set3\thxsyj\tbatch047.tar.gz\thttps://osf.io/download/68ff217699935977d04970b5/\t82c5acc860a97449eb9ab40a4acaa8c0\t3009.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch048.tar.gz\thttps://osf.io/download/68ff4e1ca743ab1938c3ffff/\te92a33c99c737b29ee5a0be50a3c1ecf\t3062.12\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch049.tar.gz\thttps://osf.io/download/68ff4b87680d8dd9f6f985a8/\t9a328ee6a256407737654c71ba3a83f7\t3055.21\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch050.tar.gz\thttps://osf.io/download/68ff509c9d683136574978a1/\t8d6ebfa8989247ae39c5d5b7b43c74d8\t3065.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch051.tar.gz\thttps://osf.io/download/68ff50538e2dab3f9119fdfd/\t6bdd28681fdd01797f67536da2ff5ce6\t3037.36\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch052.tar.gz\thttps://osf.io/download/68ff51871e852f3868f986f6/\t3920eb418a2e79495c412d8811b2a7a1\t3005.94\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch053.tar.gz\thttps://osf.io/download/68ff52bdcebefe2c2ef9845e/\t15cc752786ca6b7d3db26774a04fd87f\t3033.81\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch054.tar.gz\thttps://osf.io/download/68ff593667b36546b9f97f3e/\t5eeec63e3ae3fb5847d3fe0c4a4d3cd3\t3036.89\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch055.tar.gz\thttps://osf.io/download/68ff5c401ca7a2551819fc4b/\tcef9a8378baa10a508d83f41d40b05aa\t2988.85\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch056.tar.gz\thttps://osf.io/download/68ff5d357fd038907149707b/\t7ae6465d56769bb3078a315ae7bfd3ad\t3085.43\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch057.tar.gz\thttps://osf.io/download/68ff5e766a384dd8c77f2cb7/\t68551f09782ca6fd2d3c223d8a388972\t3052.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch058.tar.gz\thttps://osf.io/download/68ff5fad6a384dd8c77f2d6f/\t8e27f162b3a92440aa8a5147af3e3120\t3018.69\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch059.tar.gz\thttps://osf.io/download/68ff60e28fdd670e2a7f2d73/\t0e2e36d2b0c45b49f57481a58214afaf\t3007.99\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch060.tar.gz\thttps://osf.io/download/68ff621a5b66297f96f98217/\tf1429d433777c35dbb5da6b8f90a3eca\t3074.55\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch061.tar.gz\thttps://osf.io/download/68ff63570983ff67d7c4056d/\t0d606bfe794ecf59d14255af295e0a8e\t3082.74\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch062.tar.gz\thttps://osf.io/download/68ff648f8f37a9090a19ff7a/\t0e0e5725ee405a23bffff61e6aa65172\t3069.78\nAllTheBacteria/Hypothetical
+        Protein Structures/Set4\tzak4y\tbatch063.tar.gz\thttps://osf.io/download/68ff65c881df3ad7c7f97e46/\ted0631dd388e5ba23598c97b4242338c\t3055.15\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch064.tar.gz\thttps://osf.io/download/68fffdb1fcb9bdb879497022/\tdcb5b4ef49c29178c5f58a453cf56db9\t3060.03\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch065.tar.gz\thttps://osf.io/download/68fffef5b4986ff6c7f9817f/\t161cddb9e2f3e0140af4b910c6aec62f\t3028.48\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch066.tar.gz\thttps://osf.io/download/69000025e5dc081a9f497220/\tead350c4844487beaa7ac4ba561dd084\t2983.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch067.tar.gz\thttps://osf.io/download/69000159dd94b2d9307f3200/\t59afa546f7c7a77fe9cf5faf7579b001\t3035.37\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch068.tar.gz\thttps://osf.io/download/6900028f0dbc782bd4c40204/\t07a32e31c80c6a0cf2a36a33f5e39dc8\t3065.68\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch069.tar.gz\thttps://osf.io/download/690003c7fcb9bdb879497833/\t43aadf6c44889549e9f9623f46a19e27\t3044.12\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch070.tar.gz\thttps://osf.io/download/690004f99805973b6a7f2ad5/\tf6a3e4fb6f25c7988d5b00aa926adfde\t3024.71\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch071.tar.gz\thttps://osf.io/download/690006329805973b6a7f2b3e/\t0bdbb21eb141bc95d47145d384047cbd\t3057.43\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch072.tar.gz\thttps://osf.io/download/69000767fcb9bdb87949795b/\t2ce68c4d57e4dd2d1f195e033857a5fa\t3035.59\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch073.tar.gz\thttps://osf.io/download/690008985b0fb1153a7f3239/\tea21b3d51a5890e86e2a9f2575d2ce53\t2983.82\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch074.tar.gz\thttps://osf.io/download/690009d44d27537968f9839b/\td65bcac016ed3ef3278a7ea6b084ce7f\t3069.8\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch075.tar.gz\thttps://osf.io/download/69000b0cece1b4c4cdf986e6/\t98b26950520aa178ebec4862d43a71b3\t3032.39\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch076.tar.gz\thttps://osf.io/download/69000c3f50c67e23381a0186/\te647c2c22722cbc85ad2ba1347f6d79f\t3011.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch077.tar.gz\thttps://osf.io/download/69000d760dbc782bd4c407d7/\td2e8fcd726d4be99fd030939c747d41b\t3048.73\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch078.tar.gz\thttps://osf.io/download/69000ea89805973b6a7f2dba/\t45414dc9145f276987410bf65ec8dd08\t3012.4\nAllTheBacteria/Hypothetical
+        Protein Structures/Set5\t9ntgy\tbatch079.tar.gz\thttps://osf.io/download/69000fdc5b0fb1153a7f338a/\tbe66d3fe6415ea5b1124a28413aaab79\t3010.96\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch080.tar.gz\thttps://osf.io/download/69002e1933087ee35fc40689/\t019a4ef2f4f2b17a2b922bdb759e620c\t3074.39\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch081.tar.gz\thttps://osf.io/download/69002f4c77533fb55af984dd/\tb8fc1b7268c521f4ce8c981d4761ebf7\t3050.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch082.tar.gz\thttps://osf.io/download/6900307efe5543131949722d/\tc81d788151bd64fd773b63b9ce78a909\t3006.79\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch083.tar.gz\thttps://osf.io/download/690031b6afea32ad157f2c0e/\teb70eddd2de48056fae0e4e335a58581\t3068.07\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch084.tar.gz\thttps://osf.io/download/690032e3e9177e17fe4975b5/\tc6a4351ad256b3053650224866315510\t2995.82\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch085.tar.gz\thttps://osf.io/download/69003419fe554313194972d6/\tb515b1a1409780f7f5499cf7500da014\t3033.98\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch086.tar.gz\thttps://osf.io/download/690035546d0bea46b0f98284/\tc8e14503d9be0dcf13cb0f0c80a66851\t3094.99\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch087.tar.gz\thttps://osf.io/download/690036865ece85c294c40379/\t97df34cc486087e43b6d12aa587d8ccc\t3033.84\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch088.tar.gz\thttps://osf.io/download/690037b71aea2afeac7f32b6/\tdf3a9886bb69fd187b8fbd2c15336fb0\t3022.14\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch089.tar.gz\thttps://osf.io/download/690038f1a745ae8daf7f27d0/\t90944d95178b5a3401e3b2c05c5ef0a5\t3116.02\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch090.tar.gz\thttps://osf.io/download/69003a285ece85c294c40523/\t37a0f9a48a4ba77c30c7347fd7166fe6\t3076.5\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch091.tar.gz\thttps://osf.io/download/69003b5ae12b5f7e55c3fc8a/\ta281ec2388226d0ada9f32e1a34b85bd\t3018.18\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set6\tybs2x\tbatch093.tar.gz\thttps://osf.io/download/69003dce6d0bea46b0f98456/\t94190534d49ff88064f47306d586729d\t3075.01\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch094.tar.gz\thttps://osf.io/download/69003efe4241085c1b4977d4/\t8ca221c914d63b27776aa0d5b668b007\t3009.6\nAllTheBacteria/Hypothetical
+        Protein Structures/Set6\tybs2x\tbatch095.tar.gz\thttps://osf.io/download/6900402ee02f38aecd49703c/\t32ace265f198c9ce48e95cecd5e3f33d\t3007.13\nAllTheBacteria/Hypothetical
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+        Protein Structures/Set7\t3ns7e\tbatch097.tar.gz\thttps://osf.io/download/69004e3078f346092319fc71/\tae3e082ce7307feebd9e591c147318eb\t3057.86\nAllTheBacteria/Hypothetical
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046e1/\t9174e37497674641d9b22d2df90d8194\t43.28\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.663.cobs_classic.xz\thttps://osf.io/download/666c39240f8c8014543c948f/\te35d4f8c3adb48c8d54141e119817417\t19.22\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.664.cobs_classic.xz\thttps://osf.io/download/666c394c6b6c8e309404cf8e/\t31ce112d43bb5e65ca3c6ab79eb8b265\t177.33\nAllTheBacteria/Indexes/Phylign/Release_0.2_Set_4\tmqduz\tatb.assembly.r0.2.batch.665.cobs_classic.xz\thttps://osf.io/download/666c393965e1de5abb893df0/\t4a43e0ba59653fd25097749ace019722\t63.51\nAllTheBacteria/Indexes/sketchlib\trceq5\t0.2/atb_sketchlib_v020.skd\thttps://osf.io/download/usrcx/\t6117b38379c853f8b11f430ce2da7f99\t3303.15\nAllTheBacteria/Indexes/sketchlib\trceq5\t0.2/atb_sketchlib_v020.skm\thttps://osf.io/download/etjyu/\t422404b643d3ed7cf99b199371a410d7\t96.53\nAllTheBacteria/Indexes/sketchlib\trceq5\tAggregated/atb_sketchlib.aggregated.202408.skd\thttps://osf.io/download/92qmr/\t8c795bef62e5814e44387d5e912982ca\t4170.57\nAllTheBacteria/Indexes/sketchlib\trceq5\tAggregated/atb_sketchlib.aggregated.202408.skm\thttps://osf.io/download/nwfkc/\ta743351fe92efd8bab2df4209779e125\t122.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.103.tar.gz\thttps://osf.io/download/69951ac4f271898ad8506110/\t667b44afd96e6a40cc14dcaa903a089f\t770.72\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.104.tar.gz\thttps://osf.io/download/69951adf52855323c26caf88/\t6783bdb1a3a79a279d3925bf1f68add9\t832.44\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.105.tar.gz\thttps://osf.io/download/69951af8718b42a0936cacc5/\t1e73749ce0a449b97a4a096146cf41d8\t868.93\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.107.tar.gz\thttps://osf.io/download/69951a57d60c1a9ed3505f39/\t000104e5dba8e4032bcaca1a74d8127c\t557.52\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.108.tar.gz\thttps://osf.io/download/69951a93e425a51c05fa3bf7/\t00d9d1f7662396cb966cfa2cbf26ec88\t658.07\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.111.tar.gz\thttps://osf.io/download/69951a20d60c1a9ed3505f37/\t61da5eba73e7486a3f6a9890ef485bad\t437.96\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.130.tar.gz\thttps://osf.io/download/69951a0f7c6af22d0bfa427a/\tbb8f5ff7c2ab6360efa21e100d555bab\t186.55\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.139.tar.gz\thttps://osf.io/download/69951aa87d93b6b5866ca814/\t2d2fa6074a78bcea9fc930701af8c73d\t688.06\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.140.tar.gz\thttps://osf.io/download/69951bb846ad0a518d6caf2d/\t7dd0eb6f179d9d21298ff0a95659ac00\t1243.3\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-aa\thttps://osf.io/download/6993e501f3f21e18a2594315/\t2540c9029cbc9741c6e3a8479db42e95\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ab\thttps://osf.io/download/6993e5d2a2d0eb28e0c36346/\te306e01fb9ab285b92e089c37f68eb53\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ac\thttps://osf.io/download/6993e64492d922d571d16802/\t9337c023b8dc36b468d633e636fd4447\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ad\thttps://osf.io/download/6993e42d795c00d55a594166/\td40823125ed566c5763cd7f7108e2c66\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-ae\thttps://osf.io/download/6993e51b795c00d55a59421b/\t7ff8c8a614adaf40eccf92c767ed5b0e\t4900.0\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.146.tar.gz.part-af\thttps://osf.io/download/6993e5cbb8a39504f3c363b5/\t89a4d83ae3b3d835b4a4ce717b4542e9\t3703.99\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.15.tar.gz\thttps://osf.io/download/69951a45451c19d54b505c62/\t100906ef7809b897c71393f9a900d0e9\t509.88\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.17.tar.gz\thttps://osf.io/download/69951a30f271898ad85060e3/\t61133acde6203e6dd2244699523911c6\t453.42\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.192.tar.gz\thttps://osf.io/download/6993dc9ca2d0eb28e0c36006/\t9587aa9ebb9f1b8d00adbe047a9ec4e1\t1016.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.197.tar.gz\thttps://osf.io/download/69951b37d60c1a9ed3505f4e/\ta5057dd9f9e2c31f9e5847d2338cda44\t1150.02\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.210.tar.gz\thttps://osf.io/download/69951a69451c19d54b505c6b/\tf7c0c616f59fec798c2328c94d96efd3\t570.8\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.incr_release.202408.batch.30.tar.gz\thttps://osf.io/download/3pmqt/\t802f44abaf6b954ca051f6470a2b5282\t594.06\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.r0.2.batch.138.tar.gz\thttps://osf.io/download/69951b7b718b42a0936cacd9/\tf737d5c0ccc68e97d66df7c28801251f\t1216.78\nAllTheBacteria/MGE
+        annotation\tt753g\tatb.assembly.r0.2.batch.150.tar.gz\thttps://osf.io/download/69951b18718b42a0936cacce/\t3363a588874a0a800b78f7fbf8a579d2\t994.22\nAllTheBacteria/MGE
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index 24757965..300b6b71 100644
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+AllTheBacteria/Assembly/Incremental_release_2024-08	zy7er	atb.assembly.incr_release.202408.batch.10.tar.xz	https://osf.io/download/66d9a2958e73e77956a3cc98/	b12558bfe26ceb27f24d7afbab84066a	43.54
+AllTheBacteria/Assembly/Incremental_release_2025-05	rzsby	atb.assembly.incr_release.202505.batch.1.tar.xz	https://osf.io/download/6852bf1bd63d81dd5ceb70f6/	aac4dbdfbe62a14eb49622124f507bcf	34.02
+AllTheBacteria/Assembly/Incremental_release_2025-05	rzsby	atb.assembly.incr_release.202505.batch.10.tar.xz	https://osf.io/download/6852bf3fe1cea8734945897b/	f471f71beb528e4f97c2433154437e23	17.57
+AllTheBacteria/Assembly/Release_0.2_Set_1	h28c3	atb.assembly.r0.2.batch.1.tar.xz	https://osf.io/download/27tz5/	65973bf642ddd13bfd4ffffc37b72efb	32.67
+AllTheBacteria/Assembly/Release_0.2_Set_1	h28c3	atb.assembly.r0.2.batch.10.tar.xz	https://osf.io/download/z3vq5/	01d5bd50ae5157bcc7b9d7be40bd66ec	16.0
+AllTheBacteria/Assembly/Release_0.2_Set_2	d9tzp	atb.assembly.r0.2.batch.300.tar.xz	https://osf.io/download/jubs7/	47fca962dc897290e10b8c7d097b56c4	17.62
+AllTheBacteria/Assembly/Release_0.2_Set_2	d9tzp	atb.assembly.r0.2.batch.301.tar.xz	https://osf.io/download/6673fe7b2026e9027723dac6/	76bf05d9b0b6b01a132e07b67db113b1	7.1
+AllTheBacteria/Assembly/Reproducibility	j72bc	Assembly_pipeline/GCA_009914755.split_ref.tar.xz	https://osf.io/download/96s2h/	61e0eb7b2edb534a0e347c92a160672f	724.81
+AllTheBacteria/Assembly/Reproducibility	j72bc	Assembly_pipeline/gtdb_r214.syldb.file2species.map	https://osf.io/download/3427r/	a0e52ffc0f6f484f927c2aba6100b1a7	17.51
+AllTheBacteria/Biosynthetic_Gene_Cluster	cufb2	GECCO_v0.9.8/AllTheBacteria_v0.2/AllTheBacteria_v0.2_bgcs_split1.gbk.xz	https://osf.io/download/8q4y5/	76de02352cdc1f3dbed9e52294f7deb7	3612.21
+AllTheBacteria/Biosynthetic_Gene_Cluster	cufb2	GECCO_v0.9.8/AllTheBacteria_v0.2/AllTheBacteria_v0.2_bgcs_split2.gbk.xz	https://osf.io/download/3rx5w/	e49fe2ba418fa70eb60a9f17fe70bea3	1734.19
+AllTheBacteria/DefenseFinder	hpgac	Aggregated/defense_finder_results_202408.tsv.xz	https://osf.io/download/bmdxg/	c9545ebf3af5f65cac085deed384e490	135.7
+AllTheBacteria/DefenseFinder	hpgac	Aggregated/defense_finder_status_202408.tsv.xz	https://osf.io/download/wvsnr/	a75c23e604fcf99f2de36889beff80b8	9.31
+AllTheBacteria/Hypothetical Protein Structures/FASTA	rq6kz	all_hypotheticals_under_3000AA_unfiltered.fasta.gz_partaa	https://osf.io/download/6996a253773e9b01047afee7/	e48e308f4dd642c1350164cf0e097c19	1024.0
+AllTheBacteria/Hypothetical Protein Structures/FASTA	rq6kz	all_hypotheticals_under_3000AA_unfiltered.fasta.gz_partab	https://osf.io/download/6996a27524cdbae3b37afff8/	0c75927a9434514c3554b6d9eb0afc8d	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldcomp_Databases	wpyeh	foldcomp_db.tar.gz_partaa	https://osf.io/download/699683d1e7c282aa87655d47/	a013b69fed4d2116645022f544134929	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldcomp_Databases	wpyeh	foldcomp_db.tar.gz_partab	https://osf.io/download/699683f15ea4de93a87afcb0/	e8afaacb6d129993cec98ffcb5599b3b	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2	f3edq	foldcomp_db.tar.gz_partbv	https://osf.io/download/699cfaefbf4a163f18fef470/	d6981213bfbbf0ca836314d00c1b4cac	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldcomp_Databases/Foldcomp_Databases_Part2	f3edq	foldcomp_db.tar.gz_partbw	https://osf.io/download/699cfb521b6d2a2430ee2c87/	1ded130146662a5676a88b6b4914ed59	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldseek_Databases	fr37t	foldseek_db.tar.gz_partaa	https://osf.io/download/69965b2e805edf0ba87af9a9/	9ba9ae5d05935d82f5b95e47adf81b13	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Foldseek_Databases	fr37t	foldseek_db.tar.gz_partab	https://osf.io/download/69965d6a870e55721a7afa72/	57a02d2d7620ed98e35b3176ddc9c3e6	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Metadata	3qrey	ATB_AFDB_map_with_batches.tsv.gz	https://osf.io/download/kebs4/	beabc34b497ac5cc7a2d670791f225cf	129.95
+AllTheBacteria/Hypothetical Protein Structures/Metadata	3qrey	ATB_every_protein_with_species.tsv.gz_partaa	https://osf.io/download/4fwsm/	7237c1f91bac08245ac5445be046f4a2	1024.0
+AllTheBacteria/Hypothetical Protein Structures/Set1	sw6p8	batch001.tar.gz	https://osf.io/download/cu5v9/	e06bae944ad219bb3a34a1d0bd10f204	3042.14
+AllTheBacteria/Hypothetical Protein Structures/Set1	sw6p8	batch002.tar.gz	https://osf.io/download/69058c6973ae592cbcc184a8/	6543237399dcbdac0d376a57fc0f5cb3	3052.5
+AllTheBacteria/Hypothetical Protein Structures/Set2	jn4ah	batch017.tar.gz	https://osf.io/download/bngmy/	ea1c00456cb63b126cd822b6012c6e6d	3005.81
+AllTheBacteria/Hypothetical Protein Structures/Set2	jn4ah	batch018.tar.gz	https://osf.io/download/68feed6f982f1029c3f983ba/	ea03c4da38f98b8801ab7b1e882b1130	2991.36
+AllTheBacteria/Hypothetical Protein Structures/Set3	hxsyj	batch032.tar.gz	https://osf.io/download/68ff0f1199935977d0496ed8/	47dd670bfca3cd02fe83501bd7145d2d	3096.23
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_1	cke8n	atb.assembly.r0.2.batch.1.cobs_classic.xz	https://osf.io/download/yznvr/	530e397586f2a56eb3c4218e58bb1c08	110.66
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_1	cke8n	atb.assembly.r0.2.batch.10.cobs_classic.xz	https://osf.io/download/6666ff500f8c800ead3c979e/	20fc3eb6387e6c97661b2445bbe72ae6	68.48
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_2	5u46d	atb.assembly.r0.2.batch.132.cobs_classic.xz	https://osf.io/download/666866c10f8c8010163c9678/	abf517f35994b32918cca30e299ef0d4	933.54
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_2	5u46d	atb.assembly.r0.2.batch.133.cobs_classic.xz	https://osf.io/download/6668644e0f8c8010163c9470/	e92273e4c30db6785a7ec575d83379ec	1025.16
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_3	b96v2	atb.assembly.r0.2.batch.226.cobs_classic.xz	https://osf.io/download/dkf8t/	00115082c2b8d8700a10ef68bf8dbb61	503.91
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_3	b96v2	atb.assembly.r0.2.batch.227.cobs_classic.xz	https://osf.io/download/6668290077ff4c5699e0473a/	7259b805590c104a4f241fefd5fbbe99	604.7
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_4	mqduz	atb.assembly.r0.2.batch.419.cobs_classic.xz	https://osf.io/download/y9z8k/	6533ab3a19de76045442fa8650da9d74	290.42
+AllTheBacteria/Indexes/Phylign/Release_0.2_Set_4	mqduz	atb.assembly.r0.2.batch.420.cobs_classic.xz	https://osf.io/download/sx8gf/	5c94b3d1397df3efd48b474bd2fa94bb	302.37
+AllTheBacteria/Indexes/sketchlib	rceq5	0.2/atb_sketchlib_v020.skd	https://osf.io/download/usrcx/	6117b38379c853f8b11f430ce2da7f99	3303.15
+AllTheBacteria/Indexes/sketchlib	rceq5	0.2/atb_sketchlib_v020.skm	https://osf.io/download/etjyu/	422404b643d3ed7cf99b199371a410d7	96.53
+AllTheBacteria/MGE annotation	t753g	atb.assembly.incr_release.202408.batch.103.tar.gz	https://osf.io/download/69951ac4f271898ad8506110/	667b44afd96e6a40cc14dcaa903a089f	770.72
+AllTheBacteria/MGE annotation	t753g	atb.assembly.incr_release.202408.batch.104.tar.gz	https://osf.io/download/69951adf52855323c26caf88/	6783bdb1a3a79a279d3925bf1f68add9	832.44
+AllTheBacteria/MLST	23hx6	mlst_processed_all_samples.tsv.xz	https://osf.io/download/4bp2s/	a5586ea858ea7996c1263454fcf08ef1	11.69
+AllTheBacteria/MLST/ATB_Acinetobacter_baumannii_serotyping	vjma7	kaptive_Ab_serotypes.tsv.xz	https://osf.io/download/698d3d38ae62cb73c0e24e71/	48609fa0085497fe76da0d86d6ecd149	0.06
+AllTheBacteria/MLST/ATB_Clostridum;Sarcina_perfringens_toxinotyping	djhga	perfringotyper_Cperf_toxintypes.tsv.xz	https://osf.io/download/aq8z7/	db7f96b7e9a8785da66587a434b7878b	0.0
+AllTheBacteria/MLST/ATB_Listeria_monocytogens_LisSero_typing	9cbqg	lissero_Lm_serotypes.tsv.xz	https://osf.io/download/698d3adfae62cb73c0e24d39/	5a2ad6a0bd2f1f7919d4c751f8d28327	0.11
+AllTheBacteria/MLST/ATB_Shigella_sp_serotyping_and_species_ID	6a8mv	shigeifinder_shigella_typing.tsv.xz	https://osf.io/download/698d3e4a3d205a55cbc728c8/	8ddf12c26d3f37ecb2c80e959eae5080	0.01
+AllTheBacteria/MLST/ATB_Vibrio_parahaemolyticus_serotyping	xc26j	kaptive_Vp_serotypes.tsv.xz	https://osf.io/download/698d3c315679671ac7e24be4/	af00a3787f2ef545bb5f90a5158acca1	0.02
+AllTheBacteria/MLST/ATB_Virulence_Factors	gk7ec	vfdb_2024db_summary.tsv.xz	https://osf.io/download/8mg7w/	01158578be913513407498c39da5d8b8	44.37
+AllTheBacteria/Metadata	h7wzy	0.1/HQ_set_0.1/hq_dataset.accessions.txt.gz	https://osf.io/download/3znhb/	6f001b72101779b5ff6a556f46c9ddab	4.11
+AllTheBacteria/Metadata	h7wzy	0.1/HQ_set_0.1/hq_dataset.counts_bar_plot.pdf	https://osf.io/download/p5vkt/	a147e807f6a661b6f7f6dc856aa0465c	0.02
+AllTheBacteria/Species_Specific/Bacillus_cereus_group	8ua49	BTyper3_v3.4.0/0.2+inc-rel-2024-08/ATB_0.2+inc-rel-2024-08_Bacillus-cereus-group_BTyper3-v3.4.0_merged.tsv.gz	https://osf.io/download/uf7va/	4f02b2e8016360965b389f1bf5ca1948	0.17
+AllTheBacteria/Species_Specific/Bacillus_cereus_group	8ua49	BTyper3_v3.4.0/0.2+inc-rel-2024-08/ATB_0.2+inc-rel-2024-08_Bacillus-cereus-group_Status_File.tsv.gz	https://osf.io/download/yz8p4/	1c28768c74ea77f5617efab4a1bab09e	0.01
diff --git a/tests/data/atb/filtered_files.tsv b/tests/data/atb/filtered_files.tsv
new file mode 100644
index 00000000..6a88c6a8
--- /dev/null
+++ b/tests/data/atb/filtered_files.tsv
@@ -0,0 +1,25 @@
+project	project_id	filename	url	md5	size(MB)
+AllTheBacteria/Annotation/Bakta	zt57s	File_Lists/atb.bakta.incr_release.202408.status.tsv.gz	https://osf.io/download/2skzy/	7da48fce8e310916a072786872f475b1	14.19
+AllTheBacteria/Annotation/Bakta	zt57s	File_Lists/atb.bakta.r0.2.status.tsv.gz	https://osf.io/download/rxfks/	b7255867206dc66f2c26db31921a67a6	53.87
+AllTheBacteria/Annotation/Bakta/Incr_release.202408_Set_1	kdnwp	atb.bakta.incr_release.202408.batch.1.tar.xz	https://osf.io/download/r84xg/	a3ba0148c435f31b4de3f0b72e01075d	1378.51
+AllTheBacteria/Annotation/Bakta/Incr_release.202408_Set_1	kdnwp	atb.bakta.incr_release.202408.batch.10.tar.xz	https://osf.io/download/qxye9/	e0724b0a605da7298b802f01145d8b49	388.76
+AllTheBacteria/Annotation/Bakta/Incr_release.202408_Set_2	p4kvy	atb.bakta.incr_release.202408.batch.49.tar.xz	https://osf.io/download/nyua7/	c8871eab5ee9071b101ba7bbafa7983b	2320.01
+AllTheBacteria/Annotation/Bakta/Incr_release.202408_Set_2	p4kvy	atb.bakta.incr_release.202408.batch.50.tar.xz	https://osf.io/download/tqrs2/	887db770a7e176e644a2b413de4b07e5	2169.25
+AllTheBacteria/Annotation/Bakta/Release_0.2_Set_1	tyw72	atb.bakta.r0.2.batch.1.tar.xz	https://osf.io/download/vpg3d/	5e6ccd68f5c6a69a14dafaf599f9377e	293.86
+AllTheBacteria/Annotation/Bakta/Release_0.2_Set_1	tyw72	atb.bakta.r0.2.batch.10.tar.xz	https://osf.io/download/gbzev/	8fab65bbeadc99201a1df83f32b8c779	132.76
+AllTheBacteria/Annotation/Bakta/Release_0.2_Set_9	evurw	atb.bakta.r0.2.batch.228.tar.xz	https://osf.io/download/679b9dd3bc1fdea8290eb046/	dc061bcc2e1bb9c30887a4dfefb1b6c2	3841.85
+AllTheBacteria/Annotation/Bakta/Release_0.2_Set_9	evurw	atb.bakta.r0.2.batch.229.tar.xz	https://osf.io/download/679ba14cae64ecefd50eaea0/	db0081059366d08e8c3cd8c19857ef42	3902.73
+AllTheBacteria/Assembly	zxfmy	File_Lists/file_list.all.20240805.tsv.gz	https://osf.io/download/dw3h7/	5fc5c88a0593785341e466143a97f126	17.04
+AllTheBacteria/Assembly	zxfmy	File_Lists/file_list.all.202505.tsv.gz	https://osf.io/download/69a03f582574717cb3643d62/	0a9ee0b1efaf42b3ea9e89ce91d2b9e1	22.13
+AllTheBacteria/Assembly/Incremental_release_2024-08	zy7er	atb.assembly.incr_release.202408.batch.1.tar.xz	https://osf.io/download/bfeqh/	2e5d42de7f7f047245b4c4b78e4dabaf	61.36
+AllTheBacteria/Assembly/Incremental_release_2024-08	zy7er	atb.assembly.incr_release.202408.batch.10.tar.xz	https://osf.io/download/66d9a2958e73e77956a3cc98/	b12558bfe26ceb27f24d7afbab84066a	43.54
+AllTheBacteria/Assembly/Incremental_release_2025-05	rzsby	atb.assembly.incr_release.202505.batch.1.tar.xz	https://osf.io/download/6852bf1bd63d81dd5ceb70f6/	aac4dbdfbe62a14eb49622124f507bcf	34.02
+AllTheBacteria/Assembly/Incremental_release_2025-05	rzsby	atb.assembly.incr_release.202505.batch.10.tar.xz	https://osf.io/download/6852bf3fe1cea8734945897b/	f471f71beb528e4f97c2433154437e23	17.57
+AllTheBacteria/Assembly/Release_0.2_Set_1	h28c3	atb.assembly.r0.2.batch.1.tar.xz	https://osf.io/download/27tz5/	65973bf642ddd13bfd4ffffc37b72efb	32.67
+AllTheBacteria/Assembly/Release_0.2_Set_1	h28c3	atb.assembly.r0.2.batch.10.tar.xz	https://osf.io/download/z3vq5/	01d5bd50ae5157bcc7b9d7be40bd66ec	16.0
+AllTheBacteria/Assembly/Release_0.2_Set_2	d9tzp	atb.assembly.r0.2.batch.300.tar.xz	https://osf.io/download/jubs7/	47fca962dc897290e10b8c7d097b56c4	17.62
+AllTheBacteria/Assembly/Release_0.2_Set_2	d9tzp	atb.assembly.r0.2.batch.301.tar.xz	https://osf.io/download/6673fe7b2026e9027723dac6/	76bf05d9b0b6b01a132e07b67db113b1	7.1
+AllTheBacteria/Assembly/Reproducibility	j72bc	Assembly_pipeline/GCA_009914755.split_ref.tar.xz	https://osf.io/download/96s2h/	61e0eb7b2edb534a0e347c92a160672f	724.81
+AllTheBacteria/Assembly/Reproducibility	j72bc	Assembly_pipeline/gtdb_r214.syldb.file2species.map	https://osf.io/download/3427r/	a0e52ffc0f6f484f927c2aba6100b1a7	17.51
+AllTheBacteria/Metadata	h7wzy	0.1/HQ_set_0.1/hq_dataset.accessions.txt.gz	https://osf.io/download/3znhb/	6f001b72101779b5ff6a556f46c9ddab	4.11
+AllTheBacteria/Metadata	h7wzy	0.1/HQ_set_0.1/hq_dataset.counts_bar_plot.pdf	https://osf.io/download/p5vkt/	a147e807f6a661b6f7f6dc856aa0465c	0.02
diff --git a/tests/data/atb/invalid_atb_files.tsv b/tests/data/atb/invalid_atb_files.tsv
new file mode 100644
index 00000000..1be8252b
--- /dev/null
+++ b/tests/data/atb/invalid_atb_files.tsv
@@ -0,0 +1,19 @@
+<!doctype html>
+<html lang="en" data-beasties-container="">
+  <head>
+    <meta charset="utf-8">
+    <title>OSF</title>
+    <base href="/">
+    <meta name="description" content="">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <link rel="icon" type="image/x-icon" href="favicon.ico">
+    <script src="assets/ace-builds/ace.js" defer=""></script>
+    <script src="assets/js/newrelic/newrelic.snippet.js"></script>
+  <style>@-webkit-keyframes fa-spin{0%{-webkit-transform:rotate(0deg);transform:rotate(0)}to{-webkit-transform:rotate(359deg);transform:rotate(359deg)}}:root{--openSans:"Open Sans", sans-serif;--pr-blue-1:#337ab7;--pr-blue-2:#84aed2;--pr-blue-3:#0089ff;--dark-blue-1:#24384a;--dark-blue-2:#384b5c;--bg-blue-2:#e6f1fc;--bg-blue-3:#f1f8fd;--grey-1:#8b97a4;--grey-2:#e0e1e2;--grey-3:#eff0f1;--grey-4:#606b7b;--grey-outline:#00000029;--white:#ffffff;--green-1:#357935;--green-2:#d7e4d7;--green-3:#26ac26;--red-1:#b73333;--red-2:#f1d6d6;--red-3:#e40303;--yellow-1:#8a6d3a;--yellow-2:#fcf8e3;--green-1-alt:#37b183;--green-2-alt:#35aea9;--blue-1:#3792b1;--blue-2:#3379b7;--green-1-bg:#ebf7f3;--green-2-bg:#ebf7f6;--blue-1-bg:#ebf4f7;--blue-2-bg:#ebf2f8;--white-60:rgba(256, 256, 256, .6);--osf-provider-primary-color:#f5fafd;--osf-provider-secondary-color:#204762;--gradient-1:linear-gradient( 90.12deg, rgba(219, 237, 251, .5) .03%, rgba(239, 244, 252, .5) 54.38%, rgba(219, 237, 251, .5) 98.07% ), #ffffff;--gradient-2:linear-gradient( 90.12deg, rgba(219, 237, 251, .5) .03%, rgba(239, 244, 252, .5) 54.38%, rgba(219, 237, 251, .5) 98.07% ), #f3f8fd;--gradient-3:linear-gradient(90.12deg, #dbedfb .03%, #eff4fc 54.38%, #dbedfb 98.07%);--p-form-field-color:var(--dark-blue-1);--p-form-field-border-color:var(--grey-2);--p-form-field-hover-border-color:var(--grey-1);--p-form-field-disabled-background:var(--white);--p-form-field-disabled-color:var(--grey-1);--p-form-field-placeholder-color:var(--grey-4);--p-list-option-color:var(--dark-blue-1);--p-list-option-focus-color:var(--dark-blue-1);--p-list-option-focus-background:var(--bg-blue-3);--p-list-option-selected-background:var(--bg-blue-2);--stepper-step-background:var(--white);--stepper-active-step-background:var(--pr-blue-1);--stepper-step-color:var(--dark-blue-1);--stepper-active-step-color:var(--white);--stepper-space-line-color:var(--white);--stepper-active-space-line-color:var(--pr-blue-1);--stepper-step-border-color:var(--white);--stepper-active-step-border-color:var(--pr-blue-1);--stepper-invalid-step-background:var(--white);--stepper-invalid-step-color:var(--red-1);--stepper-invalid-step-border-color:var(--red-1);--header-color:none;--header-background-color:none;--header-background-image-url:none;--branding-primary-color:var(--osf-provider-primary-color);--branding-secondary-color:var(--osf-provider-secondary-color);--branding-background-color:var(--white);--branding-hero-logo-image-url:none;--branding-hero-background-image-url:none}@layer reset,base,primeng;@layer reset{*{margin:0;padding:0;box-sizing:border-box}html,body{color:var(--dark-blue-1);font-family:var(--openSans);font-weight:400;font-size:16px;max-height:100vh;max-width:100vw}body{font-size:.875rem}}@layer base{*:focus-visible{outline:1px solid var(--pr-blue-1);outline-offset:2px}}:root{--p-button-padding-x:1rem;--p-button-padding-y:.5625rem;--p-button-label-font-weight:700;--p-button-raised-shadow:0 0 4px 0 var(--grey-outline)}:root{--p-tooltip-max-width:20rem}:root{--fa-style-family-brands:"Font Awesome 6 Brands";--fa-font-brands:normal 400 1em/1 "Font Awesome 6 Brands"}@font-face{font-family:"Font Awesome 6 Brands";font-style:normal;font-weight:400;font-display:block;src:url("./media/fa-brands-400-Q3XCMWHQ.woff2") format("woff2"),url("./media/fa-brands-400-R2XQZCET.ttf") format("truetype")}:root{--fa-font-regular:normal 400 1em/1 "Font Awesome 6 Free"}@font-face{font-family:"Font Awesome 6 Free";font-style:normal;font-weight:400;font-display:block;src:url("./media/fa-regular-400-QSNYFYRT.woff2") format("woff2"),url("./media/fa-regular-400-XUOPSR7E.ttf") format("truetype")}:root{--fa-style-family-classic:"Font Awesome 6 Free";--fa-font-solid:normal 900 1em/1 "Font Awesome 6 Free"}@font-face{font-family:"Font Awesome 6 Free";font-style:normal;font-weight:900;font-display:block;src:url("./media/fa-solid-900-5ZUYHGA7.woff2") format("woff2"),url("./media/fa-solid-900-PJNKLK6W.ttf") format("truetype")}</style><link rel="stylesheet" href="styles-NSU3B3Q3.css" media="print" onload="this.media='all'"><noscript><link rel="stylesheet" href="styles-NSU3B3Q3.css"></noscript></head>
+  <body ngcm="">
+    <osf-root></osf-root>
+    <script>
+      window.prerenderReady = false;
+    </script>
+  <script src="polyfills-6YOLJV4E.js" type="module"></script><script src="scripts-4ZPDB5KD.js" defer=""></script><script src="main-6FKISB2R.js" type="module"></script></body>
+</html>
diff --git a/tests/pipelines/conftest.py b/tests/pipelines/conftest.py
index 52c78b53..4fefeae0 100644
--- a/tests/pipelines/conftest.py
+++ b/tests/pipelines/conftest.py
@@ -1,14 +1,116 @@
 """Shared fixtures for pipelines tests."""
 
-from collections.abc import Generator
+import logging
 from itertools import batched
 from pathlib import Path
 from typing import Any
-from unittest.mock import MagicMock, patch
+from unittest.mock import MagicMock
 
+import dlt
+import dlt.common.configuration.accessors
 import pytest
+from frozendict import frozendict
 
 from cdm_data_loaders.pipelines import core
+from cdm_data_loaders.pipelines.all_the_bacteria import AtbSettings
+from cdm_data_loaders.pipelines.cts_defaults import (
+    DEFAULT_CTS_SETTINGS,
+    DEFAULT_START_AT,
+    VALID_DESTINATIONS,
+    BatchedFileInputSettings,
+    CtsSettings,
+)
+from cdm_data_loaders.pipelines.ncbi_rest_api import NcbiSettings
+from cdm_data_loaders.pipelines.uniprot_kb import UniProtSettings
+from cdm_data_loaders.pipelines.uniref import UnirefSettings
+
+CASSETTES_DIR = "tests/cassettes"
+
+START_AT_VALUE = 50
+START_AT_STRING = "50"
+
+TEST_DLT_CONFIG = frozendict(
+    {
+        "destination.local_fs.bucket_url": "/output_dir",
+        "destination.local_fs.destination_type": "filesystem",
+        "destination.s3.bucket_url": "s3://some/s3/bucket",
+        "destination.s3.destination_type": "filesystem",
+        "normalize.data_writer.disable_compression": False,
+    }
+)
+
+
+DESTINATION_OUTPUT = TEST_DLT_CONFIG[f"destination.{DEFAULT_CTS_SETTINGS['use_destination']}.bucket_url"]
+
+DEFAULT_CTS_SETTINGS_RECONCILED = frozendict(
+    {
+        **DEFAULT_CTS_SETTINGS,
+        "output": DESTINATION_OUTPUT,
+        "raw_data_dir": f"{DESTINATION_OUTPUT}/raw_data",
+        "pipeline_dir": None,
+    }
+)
+
+DEFAULT_BATCH_FILE_SETTINGS_RECONCILED = frozendict({**DEFAULT_CTS_SETTINGS_RECONCILED, "start_at": DEFAULT_START_AT})
+
+TEST_CTS_SETTINGS = frozendict(
+    {
+        "dev_mode": "false",
+        "input_dir": "/dir/path",
+        "output": "/some/dir",
+        "use_destination": VALID_DESTINATIONS[1],
+        "use_output_dir_for_pipeline_metadata": "true",
+    }
+)
+
+TEST_CTS_SETTINGS_EXPECTED = frozendict(
+    {
+        **TEST_CTS_SETTINGS,
+        "dev_mode": False,
+        "use_output_dir_for_pipeline_metadata": True,
+    }
+)
+
+TEST_CTS_SETTINGS_RECONCILED = frozendict(
+    {**TEST_CTS_SETTINGS_EXPECTED, "pipeline_dir": "/some/dir/.dlt_conf", "raw_data_dir": "/some/dir/raw_data"}
+)
+
+TEST_BATCH_FILE_SETTINGS = frozendict(
+    **TEST_CTS_SETTINGS,
+    start_at=START_AT_STRING,
+)
+
+TEST_BATCH_FILE_SETTINGS_EXPECTED = frozendict(
+    **TEST_CTS_SETTINGS_EXPECTED,
+    start_at=START_AT_VALUE,
+)
+TEST_BATCH_FILE_SETTINGS_RECONCILED = frozendict(
+    {**TEST_BATCH_FILE_SETTINGS_EXPECTED, "pipeline_dir": "/some/dir/.dlt_conf", "raw_data_dir": "/some/dir/raw_data"}
+)
+
+
+DEFAULT_VCR_CONFIG = frozendict(
+    {
+        "cassette_library_dir": CASSETTES_DIR,
+        "record_mode": "once",  # record on first run, replay thereafter
+        "serializer": "yaml",
+        "match_on": ["method", "scheme", "host", "path", "query"],
+        # strip the NCBI API key from cassettes
+        "filter_query_parameters": ["api_key"],
+        "filter_headers": ["api_key"],
+        "decode_compressed_response": True,
+        "allow_playback_repeats": True,
+    }
+)
+
+
+@pytest.fixture(autouse=True)
+def logging_setup(caplog: pytest.LogCaptureFixture) -> None:
+    """Ensure that the dlt logger propagates logs to the root logger, is set to INFO, and that any messages are cleared."""
+    logger = logging.getLogger("dlt")
+    logger.propagate = True
+    caplog.set_level(logging.INFO)
+    caplog.clear()
 
 
 def make_batcher(files: list[Path], batch_size: int = 5) -> MagicMock:
@@ -19,6 +121,58 @@ def make_batcher(files: list[Path], batch_size: int = 5) -> MagicMock:
     return mock_batcher
 
 
+def _generate_dlt_config() -> dict[str, Any]:
+    """Return a fresh DLT config dict (same shape as the conftest fixture)."""
+    return {
+        "destination": {"local_fs": {"bucket_url": "/output_dir"}, "s3": {"bucket_url": "s3://my-bucket/output"}},
+        "destination.local_fs.bucket_url": "/output_dir",
+        "destination.s3.bucket_url": "s3://my-bucket/output",
+        "normalize.data_writer.disable_compression": False,
+    }
+
+
+def make_settings(
+    settings_cls: type[CtsSettings],
+    dlt_config: dict[str, Any] | None = None,
+    **kwargs: str | int | Path | dict[str, Any] | dlt.common.configuration.accessors._ConfigAccessor,
+) -> CtsSettings | BatchedFileInputSettings | NcbiSettings | AtbSettings:
+    """Generate a validated Settings object."""
+    return settings_cls(**{"dlt_config": dlt_config, **kwargs})
+
+
+def make_settings_autofill_config(
+    settings_cls: type[CtsSettings],
+    **kwargs: str | int | Path | dict[str, Any] | bool | dlt.common.configuration.accessors._ConfigAccessor | None,
+) -> CtsSettings | BatchedFileInputSettings | NcbiSettings | AtbSettings | UniProtSettings | UnirefSettings:
+    """Generate a validated Settings object, supplying the dlt_config if necessary."""
+    if not kwargs:
+        kwargs = {}
+    if "dlt_config" not in kwargs:
+        kwargs["dlt_config"] = _generate_dlt_config()
+    return settings_cls.model_validate(kwargs)
+
+
+def check_settings(
+    settings_object: CtsSettings,
+    expected: dict[str, Any] | frozendict,
+) -> None:
+    """Check that the settings object has the expected values."""
+    assert settings_object.dlt_config is not None
+    assert settings_object.model_dump(exclude={"dlt_config"}) == expected
+
+    # make sure we have both raw_data_dir and pipeline_dir
+    assert "raw_data_dir" in expected
+    assert "pipeline_dir" in expected
+    for attr, value in expected.items():
+        assert getattr(settings_object, attr) == value
+
+
+@pytest.fixture
+def dlt_config() -> dict[str, Any]:
+    """DLT config for testing purposes."""
+    return _generate_dlt_config()
+
+
 @pytest.fixture
 def fake_files() -> list[Path]:
     """List of five files, used for testing."""
@@ -26,34 +180,33 @@ def fake_files() -> list[Path]:
 
 
 @pytest.fixture
-def mock_dlt(monkeypatch: pytest.MonkeyPatch) -> MagicMock:
+def mock_dlt(monkeypatch: pytest.MonkeyPatch, dlt_config: dict[str, Any]) -> MagicMock:
     """Patch dlt in core, wiring pipeline.return_value to a fresh MagicMock."""
     dlt_mock = MagicMock()
     # patch the slack_incoming_hook config value so that tests do not send slack notifications
-    mock_slack_hook = MagicMock(slack_incoming_hook=None)
-    dlt_mock.pipeline.return_value = MagicMock(runtime_config=mock_slack_hook)
+    dlt_mock.pipeline.return_value.runtime_config.slack_incoming_hook = None
+    # patch the config in case dlt is used when initialising a settings object
+    dlt_mock.config = dlt_config
     monkeypatch.setattr(core, "dlt", dlt_mock)
-
     return dlt_mock
 
 
 @pytest.fixture
-def patched_io() -> Generator[tuple[MagicMock, MagicMock], Any]:
-    """Patch BatchCursor and stream_xml_file in core, yielding (mock_batcher_cls, mock_stream)."""
-    with (
-        patch("cdm_data_loaders.pipelines.core.BatchCursor") as mock_batcher_cls,
-        patch("cdm_data_loaders.pipelines.core.stream_xml_file") as mock_stream,
-    ):
-        mock_batcher_cls.return_value = make_batcher([])
-        yield mock_batcher_cls, mock_stream
+def patched_io(monkeypatch: pytest.MonkeyPatch) -> tuple[MagicMock, MagicMock]:
+    """Patch BatchCursor and stream_xml_file inside core; return (mock_batcher_cls, mock_stream)."""
+    mock_batcher_cls = MagicMock()
+    mock_stream = MagicMock(return_value=[])
+    monkeypatch.setattr(core, "BatchCursor", mock_batcher_cls)
+    monkeypatch.setattr(core, "stream_xml_file", mock_stream)
+    return mock_batcher_cls, mock_stream
 
 
 @pytest.fixture
-def patched_io_empty_batcher() -> Generator[tuple[MagicMock, MagicMock], Any]:
-    """Patch BatchCursor to yield no files and stream_xml_file in core, yielding (mock_batcher_cls, mock_stream)."""
-    with (
-        patch("cdm_data_loaders.pipelines.core.BatchCursor") as mock_batcher_cls,
-        patch("cdm_data_loaders.pipelines.core.stream_xml_file") as mock_stream,
-    ):
-        mock_batcher_cls.return_value.get_batch.return_value = []
-        yield mock_batcher_cls, mock_stream
+def patched_io_empty_batcher(monkeypatch: pytest.MonkeyPatch) -> tuple[MagicMock, MagicMock]:
+    """Like patched_io but BatchCursor immediately returns an empty batch."""
+    mock_batcher_cls = MagicMock()
+    mock_stream = MagicMock(return_value=[])
+    mock_batcher_cls.return_value = make_batcher([])
+    monkeypatch.setattr(core, "BatchCursor", mock_batcher_cls)
+    monkeypatch.setattr(core, "stream_xml_file", mock_stream)
+    return mock_batcher_cls, mock_stream
diff --git a/tests/pipelines/test_all_the_bacteria.py b/tests/pipelines/test_all_the_bacteria.py
new file mode 100644
index 00000000..cec1f4e2
--- /dev/null
+++ b/tests/pipelines/test_all_the_bacteria.py
@@ -0,0 +1,382 @@
+"""Tests for the all_the_bacteria pipeline."""
+
+import csv
+import logging
+from collections.abc import Callable
+from pathlib import Path
+from typing import Any
+from unittest.mock import MagicMock, call, patch
+
+import pytest
+from requests.exceptions import HTTPError
+
+from cdm_data_loaders.pipelines import all_the_bacteria, core
+from cdm_data_loaders.pipelines.all_the_bacteria import (
+    DATASET_NAME,
+    AtbSettings,
+    cli,
+    download_atb_index_tsv,
+    get_file_download_links,
+    osf_file_downloader,
+    run_atb_pipeline,
+)
+from cdm_data_loaders.pipelines.cts_defaults import VALID_DESTINATIONS
+from cdm_data_loaders.utils.download.core import NonRetryableDownloadError
+from tests.pipelines.conftest import CASSETTES_DIR
+
+
+@pytest.fixture(autouse=True)
+def patch_dlt_config(dlt_config: dict[str, Any], monkeypatch: pytest.MonkeyPatch) -> None:
+    """Monkeypatch the dlt config in all tests."""
+    monkeypatch.setattr(core.dlt, "config", dlt_config)
+
+
+@pytest.fixture(scope="module")
+def vcr_config() -> dict[str, Any]:
+    """VCR config for tests that make HTTP requests."""
+    return {
+        "cassette_library_dir": CASSETTES_DIR,
+        "record_mode": "once",  # record on first run, replay thereafter
+        "serializer": "yaml",
+        "match_on": ["method", "scheme", "host", "path", "query"],
+        "decode_compressed_response": True,
+        "allow_playback_repeats": True,
+    }
+
+
+@pytest.fixture
+def test_settings(tmp_path: Path, dlt_config: dict[str, Any]) -> AtbSettings:
+    """Generate a fake settings for testing."""
+    return AtbSettings(dlt_config=dlt_config, output=str(tmp_path))
+
+
+def test_cli_calls_run_ncbi_pipeline(monkeypatch: pytest.MonkeyPatch, dlt_config: dict[str, Any]) -> None:
+    """Ensure that cli() calls run_ncbi_pipeline with the settings."""
+    mock_settings_instance = MagicMock()
+    mock_settings_cls = MagicMock(return_value=mock_settings_instance)
+    mock_run_atb_pipeline = MagicMock()
+
+    monkeypatch.setattr(all_the_bacteria, "AtbSettings", mock_settings_cls)
+    monkeypatch.setattr(all_the_bacteria, "run_atb_pipeline", mock_run_atb_pipeline)
+
+    cli()
+
+    mock_settings_cls.assert_called_once_with(dlt_config=dlt_config)
+    mock_run_atb_pipeline.assert_called_once_with(mock_settings_instance)
+
+
+@pytest.mark.vcr
+def test_download_atb_index_tsv_vcr(test_settings: AtbSettings) -> None:
+    """Ensure that the download_atb_index function fetches the correct file."""
+    output_file = download_atb_index_tsv(test_settings)
+    raw_data_dir = Path(test_settings.raw_data_dir)
+    assert raw_data_dir.is_dir()
+    assert output_file.exists()
+    assert output_file.parent == raw_data_dir
+
+
+@pytest.mark.vcr
+def test_download_atb_index_tsv_error_404(test_settings: AtbSettings) -> None:
+    """Ensure that a 404 response causes an error and the function to die."""
+    with pytest.raises(HTTPError, match="404 Client Error"):
+        download_atb_index_tsv(test_settings)
+
+
+@pytest.mark.vcr
+def test_download_atv_index_tsv_error_missing_key(test_settings: AtbSettings) -> None:
+    """Ensure that the lack of a download link in the response throws an error."""
+    with pytest.raises(RuntimeError, match="Could not find download URL in response from "):
+        download_atb_index_tsv(test_settings)
+
+
+def test_download_atv_index_cannot_create_dir(dlt_config: dict[str, Any]) -> None:
+    """Ensure that the output raw_data_dir directory can be saved to."""
+    with pytest.raises(OSError, match=r"(Read-only file system|Permission denied)"):
+        download_atb_index_tsv(AtbSettings(dlt_config=dlt_config, output="/path/to/file"))
+
+
+@pytest.mark.vcr
+def test_download_atv_index_tsv_error_cannot_download_tsv(test_settings: AtbSettings) -> None:
+    """Ensure that the lack of a download link in the response throws an error."""
+    with pytest.raises(NonRetryableDownloadError, match="Client error: 404 Not Found"):
+        download_atb_index_tsv(test_settings)
+
+
+def test_get_file_download_links() -> None:
+    """Ensure that the appropriate files are picked out of the ATB file index TSV file."""
+    file_path = Path("tests") / "data" / "atb" / "all_atb_files.tsv"
+    filtered_files = list(get_file_download_links(file_path))
+    # load the expected results
+    expected = Path("tests") / "data" / "atb" / "filtered_files.tsv"
+    with expected.open() as fh:
+        reader = csv.DictReader(fh, delimiter="\t")
+        expected_files = list(reader)
+    assert len(filtered_files[0]) > 1
+    assert filtered_files[0] == expected_files
+
+
+def test_get_file_download_links_invalid_file(caplog: pytest.LogCaptureFixture) -> None:
+    """Ensure that the correct fields are present in the ATB TSV file and throw an error if not."""
+    file_path = Path("tests") / "data" / "atb" / "invalid_atb_files.tsv"
+    with pytest.raises(RuntimeError, match="Missing required ATB file index TSV headers"):
+        list(get_file_download_links(file_path))
+    records = caplog.records
+    assert records[-1].levelno == logging.ERROR
+    assert records[-1].message.startswith(
+        "Missing required ATB file index TSV headers: ['filename', 'md5', 'project', 'url']"
+    )
+    assert records[-2].levelno == logging.WARNING
+    assert records[-2].message.startswith("ATB file index TSV headers have changed.")
+
+
+def test_get_file_download_links_empty_file(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
+    """Ensure that an empty file causes a runtime error."""
+    file_path = tmp_path / "fake_file.tsv"
+    file_path.touch()
+    with pytest.raises(RuntimeError, match=f"No valid TSV data found in {file_path!s}"):
+        list(get_file_download_links(file_path))
+    records = caplog.records
+    assert records[-1].levelno == logging.ERROR
+    assert records[-1].message == f"No valid TSV data found in {file_path!s}"
+
+
+def test_get_file_download_links_no_file() -> None:
+    """Ensure an error is thrown if the file cannot be found."""
+    file_path = Path("/path") / "to" / "file"
+    with pytest.raises(FileNotFoundError, match="No such file or directory"):
+        list(get_file_download_links(file_path))
+
+
+# osf_file_downloader tests
+@pytest.mark.parametrize(
+    ("atb_file_list", "expected_calls", "expected_paths"),
+    [
+        (
+            [
+                {"filename": "file1.txt", "url": "https://osf.io/file1", "md5": "md5sum1"},
+                {"filename": "file2.txt", "url": "https://osf.io/file2", "md5": "md5sum2"},
+            ],
+            [
+                (
+                    "https://osf.io/file1",
+                    "file1.txt",
+                    "md5sum1",
+                ),
+                (
+                    "https://osf.io/file2",
+                    "file2.txt",
+                    "md5sum2",
+                ),
+            ],
+            ["file1.txt", "file2.txt"],
+        ),
+    ],
+)
+def test_osf_file_downloader_success(
+    test_settings: AtbSettings,
+    atb_file_list: list[dict[str, Any]],
+    expected_calls: list[tuple[str, str, str]],
+    expected_paths: list[str],
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Ensure that the osf_file_downloader function correctly calls the download client for each file."""
+    mock_download_client = MagicMock()
+    mock_logger = MagicMock()
+    with (
+        patch("cdm_data_loaders.pipelines.all_the_bacteria.FileDownloader", return_value=mock_download_client),
+        patch("cdm_data_loaders.pipelines.all_the_bacteria.logger", mock_logger),
+    ):
+        output = list(osf_file_downloader(test_settings, atb_file_list))
+
+    for item, filename in zip(atb_file_list, expected_paths, strict=True):
+        assert item["path"] == str(Path(test_settings.raw_data_dir) / filename)
+
+    assert output[0].data == [
+        {**f, "path": str(Path(test_settings.raw_data_dir) / f["filename"])} for f in atb_file_list
+    ]
+
+    assert mock_download_client.download.call_count == len(expected_calls)
+
+    for url, filename, checksum in expected_calls:
+        mock_download_client.download.assert_any_call(
+            url,
+            Path(test_settings.raw_data_dir) / filename,
+            expected_checksum=checksum,
+            checksum_fn="md5",
+        )
+
+    mock_logger.assert_not_called()
+    # no logs should be emitted for successful downloads
+    assert caplog.records == []
+
+
+@pytest.mark.parametrize(
+    ("atb_file_list", "download_side_effect", "expected_exceptions", "expected_paths"),
+    [
+        (
+            [
+                {"filename": "good_file.txt", "url": "https://osf.io/good", "md5": "md5sum1"},
+                {"filename": "great_file.txt", "url": "https://osf.io/great", "md5": "md5sum2"},
+                {"filename": "bad_file.txt", "url": "https://osf.io/bad", "md5": "badmd5"},
+            ],
+            lambda url, _save_path, **_kwargs: (
+                (_ for _ in ()).throw(RuntimeError("download failed")) if url == "https://osf.io/bad" else None
+            ),
+            ["Could not download file from https://osf.io/bad: download failed"],
+            {"good_file.txt": True, "great_file.txt": True, "bad_file.txt": False},
+        ),
+        (
+            [
+                {"filename": "bad_file.txt", "url": "https://osf.io/bad", "md5": "badmd5"},
+                {"filename": "even_worse.txt", "url": "https://osf.io/even_worse", "md5": "badmd5"},
+            ],
+            lambda _url, _save_path, **_kwargs: (_ for _ in ()).throw(Exception("Boom!")),
+            [
+                "Could not download file from https://osf.io/bad: Boom!",
+                "Could not download file from https://osf.io/even_worse: Boom!",
+            ],
+            {"bad_file.txt": False, "even_worse.txt": False},
+        ),
+    ],
+)
+def test_osf_file_downloader_error_handling(
+    test_settings: AtbSettings,
+    atb_file_list: list[dict[str, Any]],
+    download_side_effect: Callable,
+    expected_exceptions: list[str],
+    expected_paths: dict[str, bool],
+) -> None:
+    """Ensure that errors during file download are handled correctly."""
+    mock_download_client = MagicMock()
+    mock_download_client.download.side_effect = download_side_effect
+    mock_logger = MagicMock()
+
+    with (
+        patch("cdm_data_loaders.pipelines.all_the_bacteria.FileDownloader", return_value=mock_download_client),
+        patch("cdm_data_loaders.pipelines.all_the_bacteria.logger", mock_logger),
+    ):
+        list(osf_file_downloader(test_settings, atb_file_list))
+
+    for item in atb_file_list:
+        if item["filename"] in expected_paths and expected_paths[item["filename"]]:
+            assert item["path"] == str(Path(test_settings.raw_data_dir) / item["filename"])
+        else:
+            assert "path" not in item
+
+    # FIXME: why is caplog not working here? Ideally this should use caplog instead of a mock logger.
+    exception_call_args = [call.args[0] for call in mock_logger.exception.call_args_list]
+    assert exception_call_args == expected_exceptions
+
+
+def test_run_atb_pipeline(
+    test_settings: AtbSettings,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """run_atb_pipeline binds settings and delegates to run_pipeline with correct args."""
+    mock_atb_file_list = MagicMock()
+    mock_file_downloader = MagicMock()
+    mock_run_pipeline = MagicMock()
+
+    monkeypatch.setattr(all_the_bacteria, "atb_file_list", mock_atb_file_list)
+    monkeypatch.setattr(all_the_bacteria, "file_downloader", mock_file_downloader)
+    monkeypatch.setattr(all_the_bacteria, "run_pipeline", mock_run_pipeline)
+
+    output = run_atb_pipeline(test_settings)
+    assert output is None
+
+    mock_atb_file_list.bind.assert_called_once_with(test_settings)
+    mock_file_downloader.bind.assert_called_once_with(test_settings)
+    mock_run_pipeline.assert_called_once_with(
+        settings=test_settings,
+        resource=mock_file_downloader,
+        destination_kwargs={"max_table_nesting": 0},
+        pipeline_kwargs={
+            "pipeline_name": DATASET_NAME,
+            "dataset_name": DATASET_NAME,
+        },
+        pipeline_run_kwargs=None,
+    )
+
+
+def test_run_atb_pipeline_bind_order(
+    test_settings: AtbSettings,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """Both resources are bound before run_pipeline is called."""
+    call_order: list[str] = []
+
+    mock_atb_file_list = MagicMock()
+    mock_atb_file_list.bind.side_effect = lambda *_: call_order.append("atb_file_list.bind")
+
+    mock_file_downloader = MagicMock()
+    mock_file_downloader.bind.side_effect = lambda *_: call_order.append("file_downloader.bind")
+
+    def track_run_pipeline(**_: Any) -> None:
+        call_order.append("run_pipeline")
+
+    monkeypatch.setattr(all_the_bacteria, "atb_file_list", mock_atb_file_list)
+    monkeypatch.setattr(all_the_bacteria, "file_downloader", mock_file_downloader)
+    monkeypatch.setattr(all_the_bacteria, "run_pipeline", track_run_pipeline)
+
+    run_atb_pipeline(test_settings)
+
+    assert call_order.index("atb_file_list.bind") < call_order.index("run_pipeline")
+    assert call_order.index("file_downloader.bind") < call_order.index("run_pipeline")
+
+
+def test_run_atb_pipeline_resource_passed_to_run_pipeline_is_file_downloader(
+    test_settings: AtbSettings,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """The resource argument to run_pipeline is the (possibly mutated) file_downloader object."""
+    sentinel = MagicMock(name="file_downloader_sentinel")
+    mock_run_pipeline = MagicMock()
+
+    monkeypatch.setattr(all_the_bacteria, "atb_file_list", MagicMock())
+    monkeypatch.setattr(all_the_bacteria, "file_downloader", sentinel)
+    monkeypatch.setattr(all_the_bacteria, "run_pipeline", mock_run_pipeline)
+
+    run_atb_pipeline(test_settings)
+
+    assert mock_run_pipeline.call_args.kwargs["resource"] is sentinel
+
+
+@pytest.mark.parametrize("use_output_dir_for_pipeline_metadata", [True, False])
+@pytest.mark.parametrize("dev_mode", [True, False])
+def test_run_atb_pipeline_pipeline_dir_present_or_absent(
+    use_output_dir_for_pipeline_metadata: bool,
+    dev_mode: bool,
+    mock_dlt: MagicMock,
+    dlt_config: dict[str, Any],
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """Check that the appropriate args are passed as pipeline_kwargs."""
+    settings = AtbSettings(
+        dlt_config=dlt_config,
+        output="/my/output",
+        use_destination=VALID_DESTINATIONS[0],
+        use_output_dir_for_pipeline_metadata=use_output_dir_for_pipeline_metadata,
+        dev_mode=dev_mode,
+    )
+    mock_file_downloader = MagicMock(name="file_downloader")
+    if use_output_dir_for_pipeline_metadata:
+        assert settings.pipeline_dir == "/my/output/.dlt_conf"
+    else:
+        assert settings.pipeline_dir is None
+
+    monkeypatch.setattr(all_the_bacteria, "atb_file_list", MagicMock())
+    monkeypatch.setattr(all_the_bacteria, "file_downloader", mock_file_downloader)
+
+    run_atb_pipeline(settings)
+
+    assert mock_dlt.destination.call_args_list == [call(VALID_DESTINATIONS[0], max_table_nesting=0)]
+    mock_pipeline = mock_dlt.pipeline.return_value
+    assert mock_pipeline.run.call_args_list == [call(mock_file_downloader)]
+
+    pipeline_kwargs: dict[str, Any] = {"pipeline_name": DATASET_NAME, "dataset_name": DATASET_NAME}
+    if use_output_dir_for_pipeline_metadata:
+        pipeline_kwargs["pipelines_dir"] = settings.pipeline_dir
+    if dev_mode:
+        pipeline_kwargs["dev_mode"] = True
+
+    assert mock_dlt.pipeline.call_args_list == [call(destination=mock_dlt.destination.return_value, **pipeline_kwargs)]
diff --git a/tests/pipelines/test_core.py b/tests/pipelines/test_core.py
index ff8fdb93..c6d57a75 100644
--- a/tests/pipelines/test_core.py
+++ b/tests/pipelines/test_core.py
@@ -2,169 +2,449 @@
 
 import datetime
 import logging
+import os
+from collections.abc import Generator
+from copy import deepcopy
 from pathlib import Path
 from typing import Any
-from unittest.mock import MagicMock, call
+from unittest.mock import MagicMock, call, patch
 
 import pytest
 from pydantic import ValidationError
 from pydantic_settings import SettingsError
 
 from cdm_data_loaders.pipelines import core
-from cdm_data_loaders.pipelines.core import run_cli, run_pipeline, stream_xml_file_resource
+from cdm_data_loaders.pipelines.core import (
+    construct_env_var,
+    run_cli,
+    run_pipeline,
+    stream_xml_file_resource,
+    sync_configs,
+)
 from cdm_data_loaders.pipelines.cts_defaults import (
     DEFAULT_BATCH_SIZE,
+    VALID_DESTINATIONS,
     BatchedFileInputSettings,
+    CtsSettings,
 )
-from tests.pipelines.conftest import make_batcher
+from tests.pipelines.conftest import TEST_CTS_SETTINGS, _generate_dlt_config, make_batcher
+from tests.pipelines.test_cts_defaults import SETTINGS_CLASSES
+
+
+@pytest.fixture(autouse=True)
+def mock_send_slack_message(monkeypatch: pytest.MonkeyPatch) -> MagicMock:
+    """Patch send_slack_message in core to prevent undue slack notifications."""
+    slack_mock = MagicMock()
+    monkeypatch.setattr(core, "send_slack_message", slack_mock)
+    return slack_mock
+
+
+@pytest.fixture(autouse=True)
+def patch_dlt_config(dlt_config: dict[str, Any], monkeypatch: pytest.MonkeyPatch) -> None:
+    """Monkeypatch the dlt config in all tests."""
+    monkeypatch.setattr(core.dlt, "config", dlt_config)
+
+
+def make_batched_settings(**kwargs: str | int) -> BatchedFileInputSettings:
+    """Generate a validated BatchedFileInputSettings object with a valid dlt config."""
+    return BatchedFileInputSettings.model_validate({"dlt_config": _generate_dlt_config(), **kwargs})
+
 
+@pytest.fixture
+def test_bfi_settings(tmp_path: Path) -> BatchedFileInputSettings:
+    """Minimal valid BatchedFileInputSettings (no start_at, no output)."""
+    return make_batched_settings(input_dir="/fake/input", output=str(tmp_path))
 
-def make_settings(**kwargs: str | int) -> BatchedFileInputSettings:
-    """Generate a validated BatchedFileInputSettings object."""
-    return BatchedFileInputSettings.model_validate(kwargs)
+
+@pytest.fixture
+def test_cts_settings() -> CtsSettings:
+    """A fully validated CtsSettings instance using the test dlt config."""
+    return CtsSettings.model_validate({**TEST_CTS_SETTINGS, "dlt_config": _generate_dlt_config()})
 
 
 @pytest.fixture(
     params=[
         pytest.param({"input_dir": "/fake/input"}, id="default"),
         pytest.param(
-            {"input_dir": "/path/to/dir", "destination": "s3", "start_at": 15, "output": "/some/dir"},
+            {"input_dir": "/path/to/dir", "use_destination": "s3", "start_at": 15, "output": "/some/dir"},
             id="alt",
         ),
     ]
 )
 def config(request: pytest.FixtureRequest) -> BatchedFileInputSettings:
     """Parametrized fixture providing default and non-default settings."""
-    return make_settings(**request.param)
-
-
-@pytest.fixture
-def default_config() -> BatchedFileInputSettings:
-    """Minimal valid BatchedFileInputSettings (no start_at, no output)."""
-    return make_settings(input_dir="/fake/input")
-
-
-@pytest.fixture
-def fake_files() -> list[Path]:
-    """List of five files, used for testing."""
-    return [Path(f"/fake/input/part_{n}.xml") for n in [1, 2, 3, 4, 5]]
-
-
-@pytest.fixture(autouse=True)
-def mock_send_slack_message(monkeypatch: pytest.MonkeyPatch) -> MagicMock:
-    """Patch send_slack_message in core to prevent undue slack notifications."""
-    slack_mock = MagicMock()
-    monkeypatch.setattr(core, "send_slack_message", slack_mock)
-    return slack_mock
+    return make_batched_settings(**request.param)
 
 
 def assert_pipeline_run_correctly(  # noqa: PLR0913
     mock_dlt: MagicMock,
     fake_resource: MagicMock,
     destination: str,
-    destination_kwargs: dict[str, Any],
-    pipeline_kwargs: dict[str, Any],
-    pipeline_run_kwargs: dict[str, Any],
+    destination_kwargs: dict[str, Any] | None,
+    pipeline_kwargs: dict[str, Any] | None,
+    pipeline_run_kwargs: dict[str, Any] | None,
 ) -> None:
     """Shared assertion block for run_pipeline tests."""
-    assert mock_dlt.destination.call_args_list == [call(destination, **destination_kwargs)]
-    assert mock_dlt.pipeline.call_args_list == [call(destination=mock_dlt.destination.return_value, **pipeline_kwargs)]
+    assert mock_dlt.destination.call_args_list == [call(destination, **destination_kwargs or {})]
+    assert mock_dlt.pipeline.call_args_list == [
+        call(destination=mock_dlt.destination.return_value, **pipeline_kwargs or {})
+    ]
     mock_pipeline = mock_dlt.pipeline.return_value
-    assert mock_pipeline.run.call_args_list == [call(fake_resource, **pipeline_run_kwargs)]
+    assert mock_pipeline.run.call_args_list == [call(fake_resource, **pipeline_run_kwargs or {})]
+
+
+# construct_env_var
+@pytest.mark.parametrize(
+    ("b_var", "t_var", "char_str", "expected"),
+    [
+        ("B123", "T456", "C789", "https://hooks.slack.com/services/B123/T456/C789/"),
+        ("one", "two", "three", "https://hooks.slack.com/services/one/two/three/"),
+    ],
+)
+def test_construct_env_var_sets_runtime_slack_incoming_hook(
+    b_var: str, t_var: str, char_str: str, expected: str
+) -> None:
+    """Test successful setting of the RUNTIME__SLACK_INCOMING_HOOK env var when all three variables are present."""
+    with patch.dict(
+        os.environ,
+        {
+            "VARIABLE_B": b_var,
+            "VARIABLE_T": t_var,
+            "CHAR_STR": char_str,
+        },
+        clear=True,
+    ):
+        # function returns None
+        assert construct_env_var() is None
+        assert os.environ["RUNTIME__SLACK_INCOMING_HOOK"] == expected
+
+
+@pytest.mark.parametrize(
+    ("b_var", "t_var", "char_str"),
+    [
+        (None, "T456", "C789"),
+        ("B123", None, "C789"),
+        ("B123", "T456", None),
+        (None, None, None),
+        ("", "T456", "C789"),
+    ],
+)
+def test_construct_env_var_does_not_set_when_any_variable_missing(
+    b_var: str | None, t_var: str | None, char_str: str | None
+) -> None:
+    """Test unsuccessful interpolation of env vars if any of the three variables are missing or empty."""
+    env = {}
+    if b_var is not None:
+        env["VARIABLE_B"] = b_var
+    if t_var is not None:
+        env["VARIABLE_T"] = t_var
+    if char_str is not None:
+        env["CHAR_STR"] = char_str
+
+    with patch.dict(os.environ, env, clear=True):
+        assert construct_env_var() is None
+        assert "RUNTIME__SLACK_INCOMING_HOOK" not in os.environ
+
+
+def test_construct_env_var_overwrites_existing_hook() -> None:
+    """An existing RUNTIME__SLACK_INCOMING_HOOK is overwritten when all vars are present."""
+    with patch.dict(
+        os.environ,
+        {
+            "VARIABLE_B": "B",
+            "VARIABLE_T": "T",
+            "CHAR_STR": "C",
+            "RUNTIME__SLACK_INCOMING_HOOK": "https://old.hook/",
+        },
+        clear=True,
+    ):
+        assert construct_env_var() is None
+        assert os.environ["RUNTIME__SLACK_INCOMING_HOOK"] == "https://hooks.slack.com/services/B/T/C/"
+
+
+# sync_configs
+def test_sync_configs_mutates_dlt_config_in_place(dlt_config: dict[str, Any], test_cts_settings: CtsSettings) -> None:
+    """sync_configs mutates the supplied dlt_config dict in-place."""
+    original_id = id(dlt_config)
+    sync_configs(test_cts_settings, dlt_config)
+    assert id(dlt_config) == original_id
+
+
+def test_sync_configs_with_mock_dlt_config_object(test_cts_settings: CtsSettings) -> None:
+    """sync_configs works with any mapping that supports __setitem__."""
+    mock_cfg = MagicMock()
+    sync_configs(test_cts_settings, mock_cfg)
+    mock_cfg.__setitem__.assert_any_call("normalize.data_writer.disable_compression", test_cts_settings.dev_mode)
+    mock_cfg.__setitem__.assert_any_call(
+        f"destination.{test_cts_settings.use_destination}.bucket_url",
+        test_cts_settings.output,
+    )
 
 
-# run_cli tests
-def test_run_cli_success() -> None:
-    """Test that instantiating a settings object successfully allows the pipeline_fn to be run."""
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+@pytest.mark.parametrize("dev_mode", [True, False])
+@pytest.mark.parametrize("output", ["/some/path", "s3://bucket/whatever"])
+def test_sync_configs_both_keys_set_in_single_call(
+    dlt_config: dict[str, Any], test_cts_settings: CtsSettings, dev_mode: bool, use_destination: str, output: str
+) -> None:
+    """Test that sync_configs changes the disable_compression and bucket_url values."""
+    original_dlt_config = deepcopy(dlt_config)
+    test_cts_settings.dev_mode = dev_mode
+    test_cts_settings.use_destination = use_destination
+    test_cts_settings.output = output
+    sync_configs(test_cts_settings, dlt_config)
+    assert dlt_config == {
+        **original_dlt_config,
+        "normalize.data_writer.disable_compression": dev_mode,
+        f"destination.{use_destination}.bucket_url": output,
+    }
 
-    def pipeline_fn(config: Any) -> None:  # noqa: ANN401
-        assert config == "fake config object"
 
-    mock_settings_cls = MagicMock(return_value="fake config object")
+# tests for run_cli()
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_run_cli_calls_settings_cls_with_dlt_config(
+    settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure run_cli instantiates the supplied settings class with dlt.config."""
+    captured: list[CtsSettings] = []
+    original_cls = settings_cls
+
+    class _CaptureCls(original_cls):  # type: ignore[valid-type]
+        def __init__(self, **data: Any) -> None:  # noqa: ANN401
+            super().__init__(**data)
+            assert data == {"dlt_config": dlt_config}
+            captured.append(self)
+
+    run_cli(_CaptureCls, MagicMock())
+
+    assert len(captured) == 1
+    captured_config = captured[0]
+    assert isinstance(captured_config, original_cls)
+    # The object passed to sync_configs must be a fully initialised instance
+    for attr in ["dev_mode", "input_dir", "output", "use_destination", "use_output_dir_for_pipeline_metadata"]:
+        assert hasattr(captured_config, attr)
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_run_cli_function_calls_args(settings_cls: type[CtsSettings], dlt_config: dict[str, Any]) -> None:
+    """Ensure run_cli calls sync_configs with the instantiated config and dlt.config."""
+    instantiated_cls = settings_cls(dlt_config=dlt_config)
+    pipeline_fn_mock = MagicMock()
+    settings_cls_mock = MagicMock(return_value=instantiated_cls)
+
+    with (
+        patch("cdm_data_loaders.pipelines.core.construct_env_var") as mock_env_var,
+        patch("cdm_data_loaders.pipelines.core.sync_configs") as mock_sync,
+    ):
+        run_cli(settings_cls_mock, pipeline_fn_mock)  # type: ignore[reportArgumentType]
+
+    mock_env_var.assert_called_once_with()
+    settings_cls_mock.assert_called_once_with(dlt_config=dlt_config)
+    mock_sync.assert_called_once_with(instantiated_cls, dlt_config)
+    pipeline_fn_mock.assert_called_once_with(instantiated_cls)
+
+
+# error handling: SettingsError/ValidationError/ValueError
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_run_cli_reraises_settings_error(
+    settings_cls: type[CtsSettings],
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """SettingsError is printed and re-raised."""
+    err = SettingsError("bad CLI arg")
 
-    assert run_cli(mock_settings_cls, pipeline_fn) is None  # type: ignore[reportArgumentType]
-    mock_settings_cls.assert_called_once_with()
+    with (
+        patch.object(settings_cls, "__init__", side_effect=err),
+        pytest.raises(SettingsError, match="bad CLI arg"),
+    ):
+        run_cli(settings_cls, MagicMock())
 
+    log_records = caplog.records
+    assert log_records[-1].levelno == logging.ERROR
+    assert log_records[-1].message == "Error initialising config"
 
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
 @pytest.mark.parametrize(
-    "error",
+    ("bad_dlt_config", "error", "err_msg"),
     [
-        pytest.param(ValidationError("Oh no!", []), id="ValidationError"),
-        pytest.param(SettingsError("something"), id="SettingsError"),
-        pytest.param(TypeError("whatever"), id="TypeError"),
+        (None, ValidationError, "dlt_config must be defined"),
+        ({}, ValueError, "No valid destinations found in dlt configuration"),
+        ({"destination": {}}, ValueError, "No valid destinations found in dlt configuration"),
     ],
 )
-def test_run_cli_error(error: Exception) -> None:
-    """Test that a settings instantiation failure re-raises without calling pipeline_fn."""
+def test_run_cli_reraises_validation_errors(  # noqa: PLR0913
+    settings_cls: type[CtsSettings],
+    bad_dlt_config: None | dict[str, Any],
+    error: type[Exception],
+    err_msg: str,
+    caplog: pytest.LogCaptureFixture,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """Ensure that errors in instantiating the configuration are re-raised.
+
+    See also the cts_defaults test ``test_cli_app_run_dlt_config_errors``.
+    """
+    monkeypatch.setattr(core.dlt, "config", bad_dlt_config)
+    with pytest.raises(error, match=err_msg):
+        run_cli(settings_cls, MagicMock())
+
+    log_records = caplog.records
+    assert log_records[-1].levelno == logging.ERROR
+    assert log_records[-1].message == "Error initialising config"
+
+
+# error handling: unexpected Exception
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_run_cli_reraises_unexpected_exception(
+    settings_cls: type[CtsSettings], caplog: pytest.LogCaptureFixture
+) -> None:
+    """Ensure that other exceptions are caught and re-raised."""
+    boom = RuntimeError("disk on fire")
     mock_pipeline_fn = MagicMock()
-    mock_settings_cls = MagicMock(side_effect=error)
+    with (
+        patch.object(settings_cls, "__init__", side_effect=boom),
+        patch("cdm_data_loaders.pipelines.core.sync_configs") as mock_sync,
+        pytest.raises(RuntimeError, match="disk on fire"),
+    ):
+        run_cli(settings_cls, mock_pipeline_fn)
+
+    log_records = caplog.records
+    assert log_records[-1].levelno == logging.ERROR
+    assert log_records[-1].message == "Unexpected error setting up config"
+
+    mock_sync.assert_not_called()
+    mock_pipeline_fn.assert_not_called()
 
-    with pytest.raises(type(error), match=error.args[0]):
-        run_cli(mock_settings_cls, mock_pipeline_fn)  # type: ignore[reportArgumentType]
 
+# sync_configs not called on error
+@pytest.mark.parametrize(
+    "exc",
+    [
+        SettingsError("bad"),
+        ValueError("bad value"),
+    ],
+)
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_run_cli_sync_configs_not_called_on_settings_instantiation_error(
+    exc: Exception,
+    settings_cls: type[CtsSettings],
+) -> None:
+    """Ensure that further execution is stopped if settings instantiation fails."""
+    mock_pipeline_fn = MagicMock()
+    with (
+        patch.object(settings_cls, "__init__", side_effect=exc),
+        patch("cdm_data_loaders.pipelines.core.sync_configs") as mock_sync,
+        pytest.raises(type(exc)),
+    ):
+        run_cli(settings_cls, mock_pipeline_fn)
+
+    mock_sync.assert_not_called()
+    mock_sync.assert_not_called()
     mock_pipeline_fn.assert_not_called()
-    mock_settings_cls.assert_called_once_with()
 
 
-# run_pipeline tests
-def test_run_pipeline_no_output(default_config: BatchedFileInputSettings, mock_dlt: MagicMock) -> None:
-    """Ensure pipeline.run is called with correct args and dlt.config is not touched."""
-    fake_resource = MagicMock()
+def test_run_cli_uses_slack_env_var_if_set(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """RUNTIME__SLACK_INCOMING_HOOK built by construct_env_var is visible during run_cli."""
+    monkeypatch.setenv("VARIABLE_B", "BBB")
+    monkeypatch.setenv("VARIABLE_T", "TTT")
+    monkeypatch.setenv("CHAR_STR", "CCC")
 
-    run_pipeline(default_config, fake_resource)
+    run_cli(CtsSettings, MagicMock())
 
-    mock_dlt.config.__setitem__.assert_not_called()
-    assert_pipeline_run_correctly(mock_dlt, fake_resource, default_config.destination, {}, {}, {})
+    expected = "https://hooks.slack.com/services/BBB/TTT/CCC/"
+    assert os.environ.get("RUNTIME__SLACK_INCOMING_HOOK") == expected
 
 
-def test_run_pipeline_custom_output_sets_dlt_config(mock_dlt: MagicMock) -> None:
-    """Ensure a non-empty output sets the correct dlt.config bucket_url key."""
-    cfg = make_settings(output="/custom/output", destination="s3")
+def test_run_cli_no_slack_env_var_when_vars_missing(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """RUNTIME__SLACK_INCOMING_HOOK is not set when source vars are absent."""
+    for var in ("VARIABLE_B", "VARIABLE_T", "CHAR_STR", "RUNTIME__SLACK_INCOMING_HOOK"):
+        monkeypatch.delenv(var, raising=False)
+
+    run_cli(CtsSettings, MagicMock())
+
+    assert "RUNTIME__SLACK_INCOMING_HOOK" not in os.environ
+
+
+# dlt.config state after successful run
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+@pytest.mark.parametrize("dev_mode", [True, False])
+@pytest.mark.parametrize("output", ["/some/path", "s3://bucket/whatever"])
+def test_run_cli_dlt_config_updated_after_success(
+    dlt_config: dict[str, Any], settings_cls: type[CtsSettings], dev_mode: bool, use_destination: str, output: str
+) -> None:
+    """Test that sync_configs changes the disable_compression and bucket_url values."""
+    original_dlt_config = deepcopy(dlt_config)
+    settings = settings_cls(dlt_config=dlt_config, dev_mode=dev_mode, output=output, use_destination=use_destination)
+    assert settings.dev_mode == dev_mode
+    assert settings.output == output
+    assert settings.use_destination == use_destination
+    settings_cls_mock = MagicMock(return_value=settings)
+
+    run_cli(settings_cls_mock, MagicMock())  # type: ignore[reportArgumentType]
+
+    assert dlt_config == {
+        **original_dlt_config,
+        "normalize.data_writer.disable_compression": dev_mode,
+        f"destination.{use_destination}.bucket_url": output,
+    }
+
+
+# run_pipeline tests
+def test_run_pipeline_minimal(test_bfi_settings: BatchedFileInputSettings, mock_dlt: MagicMock) -> None:
+    """Ensure pipeline.run is called with correct args in the simplest case."""
     fake_resource = MagicMock()
+    run_pipeline(test_bfi_settings, fake_resource)
+    assert_pipeline_run_correctly(mock_dlt, fake_resource, test_bfi_settings.use_destination, {}, {}, {})
 
+
+@pytest.mark.parametrize("destination_kwargs", [None, {}, {"max_table_nesting": 0}])
+@pytest.mark.parametrize("pipeline_kwargs", [None, {}, {"pipeline_name": "p", "dataset_name": "d"}])
+@pytest.mark.parametrize("pipeline_run_kwargs", [None, {}, {"table_format": "delta"}])
+def test_run_pipeline_destination_pipeline_pipeline_run_kwargs_set(
+    mock_dlt: MagicMock,
+    destination_kwargs: dict[str, Any] | None,
+    pipeline_kwargs: dict[str, Any] | None,
+    pipeline_run_kwargs: dict[str, Any] | None,
+) -> None:
+    """Ensure a non-empty output sets the correct dlt.config bucket_url key."""
+    settings = make_batched_settings(input_dir="/i", output="/custom/output", use_destination="s3")
+    fake_resource = MagicMock()
     run_pipeline(
-        cfg,
+        settings,
         fake_resource,
-        pipeline_kwargs={"pipeline_name": "some pipeline", "dataset_name": "some dataset"},
-        destination_kwargs={"max_table_nesting": 0},
-        pipeline_run_kwargs={"table_format": "delta"},
+        destination_kwargs=destination_kwargs,
+        pipeline_kwargs=pipeline_kwargs,
+        pipeline_run_kwargs=pipeline_run_kwargs,
     )
-
-    mock_dlt.config.__setitem__.assert_called_once_with("destination.s3.bucket_url", "/custom/output")
     assert_pipeline_run_correctly(
         mock_dlt,
         fake_resource,
         "s3",
-        {"max_table_nesting": 0},
-        {"pipeline_name": "some pipeline", "dataset_name": "some dataset"},
-        {"table_format": "delta"},
+        destination_kwargs,
+        pipeline_kwargs,
+        pipeline_run_kwargs,
     )
 
 
-@pytest.mark.parametrize("slack_configured", [True, False])
 def test_run_pipeline_graceful_fail(
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
     mock_dlt: MagicMock,
-    mock_send_slack_message: MagicMock,
-    slack_configured: bool,
     caplog: pytest.LogCaptureFixture,
 ) -> None:
     """Ensure that errors during pipeline runs are caught and do not cause the entire pipeline to go ka-boom."""
     error = RuntimeError("Oh crap!!")
     fake_resource = MagicMock()
 
-    if slack_configured:
-        slack_hook = "http://some.url.slack.com"
-        mock_dlt.pipeline.return_value.runtime_config.slack_incoming_hook = slack_hook  # = mock_slack_hook
-
     mock_dlt.pipeline.return_value.run.side_effect = error
 
-    run_pipeline(default_config, fake_resource)
-
-    if slack_configured:
-        mock_send_slack_message.assert_called_once_with("http://some.url.slack.com", f"Pipeline failed: {error!s}")
-    else:
-        mock_send_slack_message.assert_not_called()
+    output = run_pipeline(test_bfi_settings, fake_resource)
+    assert output is None
 
     assert caplog.records[-1].levelno == logging.ERROR
     assert caplog.records[-1].message.startswith("Pipeline failed: ")
@@ -174,42 +454,161 @@ def test_run_pipeline_graceful_fail(
 
 
 @pytest.mark.parametrize("slack_configured", [True, False])
-def test_run_pipeline_slack_configured(
-    default_config: BatchedFileInputSettings,
+@pytest.mark.parametrize("success", [True, False])
+def test_run_pipeline_slack_configured(  # noqa: PLR0913
+    test_bfi_settings: BatchedFileInputSettings,
     mock_dlt: MagicMock,
     mock_send_slack_message: MagicMock,
     slack_configured: bool,
+    success: bool,
     caplog: pytest.LogCaptureFixture,
 ) -> None:
     """Test that a slack message is sent if the slack_incoming_hook runtime config value is available."""
+    # set up slack config
     if slack_configured:
         slack_hook = "http://some.url.slack.com"
-        mock_dlt.pipeline.return_value.runtime_config.slack_incoming_hook = slack_hook  # = mock_slack_hook
+        mock_dlt.pipeline.return_value.runtime_config.slack_incoming_hook = slack_hook
+
+    # set an error to be triggered if success is false
+    if not success:
+        error = RuntimeError("Oh crap!!")
+        mock_dlt.pipeline.return_value.run.side_effect = error
 
-    run_pipeline(default_config, MagicMock())
+    run_pipeline(test_bfi_settings, MagicMock())
 
     if slack_configured:
-        mock_send_slack_message.assert_called_once_with("http://some.url.slack.com", "Pipeline completed successfully!")
+        if success:
+            mock_send_slack_message.assert_called_once_with(
+                "http://some.url.slack.com", "Pipeline completed successfully!"
+            )
+        else:
+            mock_send_slack_message.assert_called_once_with("http://some.url.slack.com", f"Pipeline failed: {error!s}")
         assert "Slack webhook not configured; no Slack alerts will be sent" not in caplog.messages
     else:
         mock_send_slack_message.assert_not_called()
         assert "Slack webhook not configured; no Slack alerts will be sent." in caplog.messages
 
+    if success:
+        # log messages on success
+        assert caplog.records[-1].levelno == logging.INFO
+        assert caplog.records[-1].message.startswith("Work complete!")
+    else:
+        assert caplog.records[-1].levelno == logging.ERROR
+        assert caplog.records[-1].message.startswith("Pipeline failed: ")
+
+
+@pytest.mark.usefixtures("dlt_config")
+def test_run_pipeline_sets_pipelines_dir_when_pipeline_dir_set(mock_dlt: MagicMock) -> None:
+    """pipelines_dir is injected into pipeline_kwargs when config.pipeline_dir is set."""
+    settings = make_batched_settings(input_dir="/i", output="/out", use_output_dir_for_pipeline_metadata=True)
+    assert settings.pipeline_dir is not None
+
+    run_pipeline(settings, MagicMock())
+
+    pipeline_call_kwargs = mock_dlt.pipeline.call_args.kwargs
+    assert pipeline_call_kwargs["pipelines_dir"] == settings.pipeline_dir
+
+
+def test_run_pipeline_no_pipelines_dir_when_pipeline_dir_none(
+    test_bfi_settings: BatchedFileInputSettings, mock_dlt: MagicMock
+) -> None:
+    """pipelines_dir is absent from pipeline_kwargs when config.pipeline_dir is None."""
+    assert test_bfi_settings.pipeline_dir is None
+    run_pipeline(test_bfi_settings, MagicMock())
+    pipeline_call_kwargs = mock_dlt.pipeline.call_args.kwargs
+    assert "pipelines_dir" not in pipeline_call_kwargs
+
+
+@pytest.mark.usefixtures("dlt_config")
+def test_run_pipeline_sets_dev_mode_in_pipeline_kwargs_when_true(mock_dlt: MagicMock) -> None:
+    """dev_mode=True is forwarded to dlt.pipeline()."""
+    settings = make_batched_settings(input_dir="/i", output="/out", dev_mode=True)
+    run_pipeline(settings, MagicMock())
+    pipeline_call_kwargs = mock_dlt.pipeline.call_args.kwargs
+    assert pipeline_call_kwargs.get("dev_mode") is True
+
+
+def test_run_pipeline_dev_mode_absent_from_pipeline_kwargs_when_false(
+    test_bfi_settings: BatchedFileInputSettings, mock_dlt: MagicMock
+) -> None:
+    """dev_mode=False is NOT forwarded to dlt.pipeline() (the branch is if config.dev_mode:)."""
+    assert test_bfi_settings.dev_mode is False
+    run_pipeline(test_bfi_settings, MagicMock())
+    pipeline_call_kwargs = mock_dlt.pipeline.call_args.kwargs
+    assert "dev_mode" not in pipeline_call_kwargs
+
 
 # stream_xml_file_resource tests
+@pytest.mark.parametrize("start_at", [0, 5, 173])
+def test_stream_xml_resource_nonzero_start_at_passed_to_batcher(
+    patched_io: tuple[MagicMock, MagicMock], start_at: int
+) -> None:
+    """start_at > 0 is truthy and must be forwarded to BatchCursor."""
+    mock_batcher_cls, _ = patched_io
+    mock_batcher_cls.return_value = make_batcher([])
+    settings = make_batched_settings(input_dir="/i", start_at=start_at)
+
+    list(stream_xml_file_resource(settings, "tag", MagicMock()))
+    if start_at == 0:
+        assert "start_at" not in mock_batcher_cls.call_args.kwargs
+    else:
+        assert mock_batcher_cls.call_args.kwargs.get("start_at") == start_at
+
+
+@pytest.mark.usefixtures("mock_dlt")
+def test_stream_xml_resource_timestamp_is_utc(
+    patched_io: tuple[MagicMock, MagicMock],
+    test_bfi_settings: BatchedFileInputSettings,
+) -> None:
+    """The timestamp is set once and passed to parse_fn."""
+    files = [Path(f"/f/{i}.xml") for i in range(3)]
+    mock_batcher_cls, mock_stream = patched_io
+    mock_batcher_cls.return_value = make_batcher(files)
+    mock_stream.return_value = ["e1", "e2"]
+    mock_parse = MagicMock(return_value={})
+
+    list(stream_xml_file_resource(test_bfi_settings, "tag", mock_parse))
+
+    timestamps = {c.kwargs["timestamp"] for c in mock_parse.call_args_list}
+    assert len(timestamps) == 1
+    ts: datetime.datetime = timestamps.pop()
+    assert ts.tzinfo is datetime.UTC
+
+
+@pytest.mark.usefixtures("mock_dlt")
+@pytest.mark.parametrize("log_interval", [1, 3, 1000])
+def test_stream_xml_resource_progress_logged_at_interval(
+    patched_io: tuple[MagicMock, MagicMock],
+    test_bfi_settings: BatchedFileInputSettings,
+    log_interval: int,
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """A progress log is emitted every log_interval entries."""
+    n_entries = 6
+    fake_file = Path("/f/file.xml")
+    mock_batcher_cls, mock_stream = patched_io
+    mock_batcher_cls.return_value = make_batcher([fake_file])
+    mock_stream.return_value = [MagicMock() for _ in range(n_entries)]
+
+    list(stream_xml_file_resource(test_bfi_settings, "tag", MagicMock(return_value={}), log_interval=log_interval))
+
+    progress_msgs = [m for m in caplog.messages if m.startswith("Processed")]
+    expected_count = n_entries // log_interval
+    assert len(progress_msgs) == expected_count
+
+
 def test_stream_xml_file_resource_empty_batch_yields_nothing(
     config: BatchedFileInputSettings,
     patched_io: tuple[MagicMock, MagicMock],
     caplog: pytest.LogCaptureFixture,
 ) -> None:
     """No items yielded when BatchCursor returns an empty batch; BatchCursor receives correct args."""
-    mock_batcher_cls, mock_stream = patched_io
     mock_batcher = MagicMock()
     mock_batcher.get_batch.return_value = []
+    mock_batcher_cls, mock_stream = patched_io
     mock_batcher_cls.return_value = mock_batcher
 
     results = list(stream_xml_file_resource(config, "xml_tag", MagicMock()))
-
     assert results == []
 
     expected_batcher_kwargs = {"batch_size": DEFAULT_BATCH_SIZE}
@@ -225,7 +624,7 @@ def test_stream_xml_file_resource_empty_batch_yields_nothing(
 def test_stream_xml_file_resource_yields_items_for_each_table_in_parsed_entry(
     mock_dlt: MagicMock,
     patched_io: tuple[MagicMock, MagicMock],
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
 ) -> None:
     """One item is yielded per table key returned by the parse function."""
     fake_file = Path("/fake/input/part1.xml")
@@ -237,9 +636,9 @@ def test_stream_xml_file_resource_yields_items_for_each_table_in_parsed_entry(
     mock_batcher_cls, mock_stream = patched_io
     mock_batcher_cls.return_value = make_batcher([fake_file])
     mock_stream.return_value = [fake_entry]
-
     mock_dlt.mark.with_table_name.return_value = object()
-    results = list(stream_xml_file_resource(default_config, "xml_tag", MagicMock(return_value=parsed_entry)))
+
+    results = list(stream_xml_file_resource(test_bfi_settings, "xml_tag", MagicMock(return_value=parsed_entry)))
 
     assert len(results) == len(parsed_entry)
     actual_calls = [list(c.args) for c in mock_dlt.mark.with_table_name.call_args_list]
@@ -251,7 +650,7 @@ def test_stream_xml_file_resource_yields_items_for_each_table_in_parsed_entry(
 @pytest.mark.usefixtures("mock_dlt")
 def test_stream_xml_file_resource_parse_fn_correct_args(
     patched_io: tuple[MagicMock, MagicMock],
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
 ) -> None:
     """Ensure that parse_fn is called with (entry, timestamp, file_path) for every streamed XML entry."""
     fake_file = Path("/fake/input/part1.xml")
@@ -262,7 +661,7 @@ def test_stream_xml_file_resource_parse_fn_correct_args(
     mock_stream.return_value = mock_stream_return
     mock_parse = MagicMock(return_value={})
 
-    list(stream_xml_file_resource(default_config, xml_tag, mock_parse))
+    list(stream_xml_file_resource(test_bfi_settings, xml_tag, mock_parse))
 
     assert mock_parse.call_count == len(mock_stream_return)
     for i, c in enumerate(mock_parse.call_args_list):
@@ -277,7 +676,7 @@ def test_stream_xml_file_resource_processes_all_files_across_batches(
     patched_io: tuple[MagicMock, MagicMock],
     fake_files: list[Path],
     batch_size: int,
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
     caplog: pytest.LogCaptureFixture,
 ) -> None:
     """Ensure that stream_xml_file is called for every file regardless of batch size; file reads are logged."""
@@ -285,7 +684,7 @@ def test_stream_xml_file_resource_processes_all_files_across_batches(
     mock_batcher_cls.return_value = make_batcher(fake_files, batch_size)
     mock_stream.return_value = []
 
-    list(stream_xml_file_resource(default_config, "some_tag", MagicMock()))
+    list(stream_xml_file_resource(test_bfi_settings, "some_tag", MagicMock()))
 
     assert mock_stream.call_args_list == [call(f, "some_tag") for f in fake_files]
     assert caplog.messages == [f"Reading from {f!s}" for f in fake_files]
@@ -295,14 +694,13 @@ def test_stream_xml_file_resource_multiple_batches_with_output(  # noqa: PLR0913
     mock_dlt: MagicMock,
     patched_io: tuple[MagicMock, MagicMock],
     fake_files: list[Path],
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
     caplog: pytest.LogCaptureFixture,
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
     """End-to-end: generator processes all batches, parse output is passed to dlt.mark."""
     mock_batcher_cls, _ = patched_io
     mock_batcher_cls.return_value = make_batcher(fake_files, batch_size=2)
-    # with patch("cdm_data_loaders.pipelines.core.BatchCursor") as mock_batcher_cls:
     xml_tag = "some_tag"
     captured_output: dict[str, list[Any]] = {"entry": [], "file_path": []}
 
@@ -322,7 +720,7 @@ def store_table_output(rows: list[dict[str, Any]], table: str) -> None:
     monkeypatch.setattr(core, "stream_xml_file", fake_stream_xml_file)
     mock_dlt.mark.with_table_name.side_effect = store_table_output
 
-    output = list(stream_xml_file_resource(default_config, xml_tag, fake_parse))
+    output = list(stream_xml_file_resource(test_bfi_settings, xml_tag, fake_parse))
 
     assert len(output) == len(fake_files) * 2
     assert caplog.messages == [f"Reading from {f!s}" for f in fake_files]
@@ -334,11 +732,11 @@ def store_table_output(rows: list[dict[str, Any]], table: str) -> None:
 def test_integration_resource_and_pipeline_with_table_name_output_validated(
     mock_dlt: MagicMock,
     patched_io: tuple[MagicMock, MagicMock],
-    default_config: BatchedFileInputSettings,
+    test_bfi_settings: BatchedFileInputSettings,
     fake_files: list[Path],
 ) -> None:
     """Run test_stream_xml_file_resource_multiple_batches_with_output within the run_pipeline method."""
-    mock_batcher_cls, mock_stream = patched_io
+    mock_batcher_cls, _ = patched_io
     mock_batcher_cls.return_value = make_batcher(fake_files)
     xml_tag = "entry"
 
@@ -352,20 +750,18 @@ def fake_parse(entry: dict[str, Any], timestamp: datetime.datetime, file_path: P
         assert entry == {"file_path_from_stream_xml_file": file_path, "xml_tag": "entry"}
         return {"entry": [entry], "file_path": [file_path]}
 
-    # use the fake_stream_xml_file function to mock the output of stream_xml_file
-    mock_stream.side_effect = fake_stream_xml_file
-
     # make pipeline.run execute the stream_xml_file_resource generator
     mock_dlt.pipeline.return_value.run.side_effect = lambda resource, **_: list(resource)
 
-    resource = stream_xml_file_resource(default_config, "entry", fake_parse)
-    run_pipeline(
-        default_config,
-        resource,
-        destination_kwargs=None,
-        pipeline_kwargs={"pipeline_name": "test_pipeline_name", "dataset_name": "test_dataset_name"},
-        pipeline_run_kwargs={"table_format": "delta"},
-    )
+    resource = stream_xml_file_resource(test_bfi_settings, "entry", fake_parse)
+    with patch.object(core, "stream_xml_file", fake_stream_xml_file):
+        run_pipeline(
+            test_bfi_settings,
+            resource,
+            destination_kwargs=None,
+            pipeline_kwargs={"pipeline_name": "test_pipeline_name", "dataset_name": "test_dataset_name"},
+            pipeline_run_kwargs={"table_format": "delta"},
+        )
 
     mock_dlt.pipeline.return_value.run.assert_called_once()
     assert mock_dlt.pipeline.return_value.run.call_args_list == [call(resource, table_format="delta")]
@@ -382,111 +778,110 @@ def fake_parse(entry: dict[str, Any], timestamp: datetime.datetime, file_path: P
     assert call_args_list == expected
 
 
-# test run_cli + stream_xml_file_resource + run_pipeline
-def test_integration_cli_resource_and_pipeline_with_table_name_output_validated(
+def test_integration_empty_input_pipeline_run_still_called(
     mock_dlt: MagicMock,
-    patched_io: tuple[MagicMock, MagicMock],
-    default_config: BatchedFileInputSettings,
-    fake_files: list[Path],
+    patched_io_empty_batcher: tuple[MagicMock, MagicMock],
+    test_bfi_settings: BatchedFileInputSettings,
 ) -> None:
-    """Run test_stream_xml_file_resource_multiple_batches_with_output within the run_pipeline method."""
-    mock_batcher_cls, mock_stream = patched_io
-    mock_batcher_cls.return_value = make_batcher(fake_files)
-    xml_tag = "entry"
-
-    def fake_stream_xml_file(file_path: Path, tag: str) -> list[dict[str, Any]]:
-        assert file_path in fake_files
-        assert tag == xml_tag
-        return [{"file_path_from_stream_xml_file": file_path, "xml_tag": tag}]
+    """pipeline.run is called even when the resource yields nothing."""
+    _, mock_stream = patched_io_empty_batcher
+    resource = stream_xml_file_resource(test_bfi_settings, "entry", MagicMock(return_value={}))
+    run_pipeline(test_bfi_settings, resource, pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"})
 
-    def fake_parse(entry: dict[str, Any], timestamp: datetime.datetime, file_path: Path) -> dict[str, list[Any]]:
-        assert isinstance(timestamp, datetime.datetime)
-        assert entry == {"file_path_from_stream_xml_file": file_path, "xml_tag": xml_tag}
-        return {"entry": [entry], "file_path": [file_path]}
+    mock_stream.assert_not_called()
+    mock_dlt.mark.with_table_name.assert_not_called()
+    mock_dlt.pipeline.return_value.run.assert_called_once()
 
-    # use the fake_stream_xml_file function to mock the output of stream_xml_file
-    mock_stream.side_effect = fake_stream_xml_file
 
-    # make pipeline.run execute the stream_xml_file_resource generator
-    mock_dlt.pipeline.return_value.run.side_effect = lambda resource, **_: list(resource)
+# test run_cli + stream_xml_file_resource + run_pipeline
+@pytest.mark.use_fixtures("patched_io_empty_batcher", "test_bfi_settings")
+def test_integration_run_cli_calls_pipeline_fn_with_config(mock_dlt: MagicMock) -> None:
+    """The exact config produced by run_cli reaches stream_xml_file_resource unchanged."""
+    received: list[CtsSettings] = []
 
-    def pipeline_fn(cfg: BatchedFileInputSettings) -> None:
-        """Fake pipeline function."""
-        resource = stream_xml_file_resource(cfg, xml_tag, fake_parse)
-        run_pipeline(
-            cfg, resource, pipeline_kwargs={"pipeline_name": "test_pipeline_name", "dataset_name": "test_dataset_name"}
-        )
+    def pipeline_fn(settings: BatchedFileInputSettings) -> None:
+        received.append(settings)
+        resource = stream_xml_file_resource(settings, "entry", MagicMock(return_value={}))
+        run_pipeline(settings, resource, pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"})
 
-    run_cli(MagicMock(return_value=default_config), pipeline_fn)  # type: ignore[reportArgumentType]
+    run_cli(BatchedFileInputSettings, pipeline_fn)
 
-    mock_dlt.pipeline.assert_called_once_with(
-        pipeline_name="test_pipeline_name",
-        destination=mock_dlt.destination.return_value,
-        dataset_name="test_dataset_name",
-    )
+    assert len(received) == 1
+    assert isinstance(received[0], BatchedFileInputSettings)
     mock_dlt.pipeline.return_value.run.assert_called_once()
-    # check the output to with_table_name is correct for every file and both tables
-    call_args_list = [list(c.args) for c in mock_dlt.mark.with_table_name.call_args_list]
-    expected = []
-    for f in fake_files:
-        expected.extend(
-            [
-                [[{"file_path_from_stream_xml_file": f, "xml_tag": xml_tag}], "entry"],
-                [[f], "file_path"],
-            ]
-        )
-    assert call_args_list == expected
 
 
 @pytest.mark.usefixtures("patched_io_empty_batcher")
-def test_integration_resource_and_pipeline_custom_output(
+def test_integration_full_pipeline_config_propagated(
     mock_dlt: MagicMock,
+    config: BatchedFileInputSettings,
 ) -> None:
-    """Ensure that when output is set, dlt.config bucket_url is written and pipeline.run still executes."""
-    cfg = make_settings(output="/custom/output", destination="s3")
+    """The exact config object from run_cli reaches stream_xml_file_resource unchanged.
+
+    TODO: this test and the previous test are almost identical. Remove one or the other.
+    """
+    received: list[BatchedFileInputSettings] = []
+
+    def pipeline_fn(settings: BatchedFileInputSettings) -> None:
+        received.append(settings)
+        resource = stream_xml_file_resource(settings, "entry", MagicMock(return_value={}))
+        run_pipeline(settings, resource, pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"})
 
-    resource = stream_xml_file_resource(cfg, "entry", MagicMock(return_value={}))
-    run_pipeline(cfg, resource, pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"})
+    run_cli(MagicMock(return_value=config), pipeline_fn)  # type: ignore[reportArgumentType]
 
-    mock_dlt.config.__setitem__.assert_called_once_with("destination.s3.bucket_url", "/custom/output")
+    assert len(received) == 1
+    assert received[0] == config
     mock_dlt.pipeline.return_value.run.assert_called_once()
 
 
-def test_integration_empty_input_dir_pipeline_run_still_called(
+def test_integration_run_cli_full_xml_pipeline(
     mock_dlt: MagicMock,
-    patched_io_empty_batcher: tuple[MagicMock, MagicMock],
-    default_config: BatchedFileInputSettings,
+    patched_io: tuple[MagicMock, MagicMock],
+    fake_files: list[Path],
 ) -> None:
-    """Ensure that pipeline.run is called even when the resource generator yields nothing."""
-    _, mock_stream = patched_io_empty_batcher
+    """Full integration: run_cli => pipeline_fn => stream_xml_file_resource => run_pipeline."""
+    xml_tag = "entry"
+    mock_batcher_cls, _ = patched_io
+    mock_batcher_cls.return_value = make_batcher(fake_files)
 
-    resource = stream_xml_file_resource(default_config, "entry", MagicMock(return_value={}))
-    run_pipeline(default_config, resource, pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"})
+    def fake_stream(file_path: Path, tag: str) -> list[dict]:
+        return [{"fp": file_path, "tag": tag}]
 
-    mock_stream.assert_not_called()
-    mock_dlt.mark.with_table_name.assert_not_called()
-    mock_dlt.pipeline.return_value.run.assert_called_once()
+    def fake_parse(entry: dict, timestamp: datetime.datetime, file_path: Path) -> dict:  # noqa: ARG001
+        return {"entry": [entry], "file_path": [file_path]}
 
+    mock_dlt.pipeline.return_value.run.side_effect = lambda resource, **_: list(resource)
 
-@pytest.mark.usefixtures("patched_io_empty_batcher")
-def test_integration_full_pipeline_config_propagated(
-    mock_dlt: MagicMock,
-    config: BatchedFileInputSettings,
-) -> None:
-    """The exact config object from run_cli reaches stream_xml_file_resource unchanged."""
-    received: list[BatchedFileInputSettings] = []
+    def pipeline_fn(settings: BatchedFileInputSettings) -> None:
+        resource = stream_xml_file_resource(settings, xml_tag, fake_parse)
+        run_pipeline(settings, resource, pipeline_kwargs={"pipeline_name": "tp", "dataset_name": "td"})
 
-    def pipeline_fn(inner_cfg: BatchedFileInputSettings) -> None:
-        received.append(inner_cfg)
-        resource = stream_xml_file_resource(inner_cfg, "entry", MagicMock(return_value={}))
-        run_pipeline(
-            inner_cfg,
-            resource,
-            pipeline_kwargs={"pipeline_name": "p", "dataset_name": "d"},
-        )
+    with (
+        patch.object(core, "stream_xml_file", fake_stream),
+    ):
+        run_cli(BatchedFileInputSettings, pipeline_fn)
 
-    run_cli(MagicMock(return_value=config), pipeline_fn)  # type: ignore[reportArgumentType]
+    # pipeline instantiation
+    mock_dlt.pipeline.assert_called_once_with(
+        destination=mock_dlt.destination.return_value,
+        dataset_name="td",
+        pipeline_name="tp",
+    )
 
-    assert len(received) == 1
-    assert received[0] == config
+    # pipeline.run called once with resource (stream_xml_file_resource)
     mock_dlt.pipeline.return_value.run.assert_called_once()
+    fn = next(iter(mock_dlt.pipeline.return_value.run.call_args_list[0].args))
+    assert isinstance(fn, Generator)
+    assert fn.__name__ == "stream_xml_file_resource"  # type: ignore[reportAttributeAccessIssue]
+
+    # args to dlt.mark.with_table_name
+    actual = [list(c.args) for c in mock_dlt.mark.with_table_name.call_args_list]
+    expected = []
+    for f in fake_files:
+        expected.extend(
+            [
+                [[{"fp": f, "tag": xml_tag}], "entry"],
+                [[f], "file_path"],
+            ]
+        )
+    assert actual == expected
diff --git a/tests/pipelines/test_cts_defaults.py b/tests/pipelines/test_cts_defaults.py
index e0e2b9a3..035b81d6 100644
--- a/tests/pipelines/test_cts_defaults.py
+++ b/tests/pipelines/test_cts_defaults.py
@@ -1,95 +1,391 @@
-"""Tests for the uniprot_kb DLT pipeline."""
+"""Tests for the Settings objects used by DLT pipelines."""
+
+from pathlib import Path
+from typing import Any
 
 import pytest
 from pydantic import ValidationError
 from pydantic_settings import CliApp
 
 from cdm_data_loaders.pipelines.cts_defaults import (
-    INPUT_MOUNT,
+    ARG_ALIASES,
+    DEFAULT_START_AT,
     VALID_DESTINATIONS,
     BatchedFileInputSettings,
+    CtsSettings,
+)
+from tests.pipelines.conftest import (
+    DEFAULT_BATCH_FILE_SETTINGS_RECONCILED,
+    DEFAULT_CTS_SETTINGS_RECONCILED,
+    TEST_BATCH_FILE_SETTINGS,
+    TEST_BATCH_FILE_SETTINGS_RECONCILED,
+    TEST_CTS_SETTINGS,
+    TEST_CTS_SETTINGS_RECONCILED,
+    check_settings,
+    make_settings,
 )
 
-START_AT_VALUE = 50
-START_AT_STRING = "50"
+SETTINGS_CLASSES = [CtsSettings, BatchedFileInputSettings]
 
+INVALID_DESTINATIONS = ["gcs", "filesystem", "", "LocalFs", "S3"]
+INVALID_BOOLEAN_VALUES = ["what", "yep", "nope", "2", -1, "", " ", "wtf", None]
 
-def make_settings(**kwargs: str | int) -> BatchedFileInputSettings:
-    """Generate a validated Settings object."""
-    return BatchedFileInputSettings.model_validate(kwargs)
+# a whole load of values that Pydantic will coerce to a boolean
+TRUE_FALSE_VALUES = [
+    ("0", False),
+    ("1", True),
+    ("f", False),
+    ("false", False),
+    ("False", False),
+    ("FALSE", False),
+    ("n", False),
+    ("no", False),
+    ("off", False),
+    ("on", True),
+    ("t", True),
+    ("true", True),
+    ("True", True),
+    ("TRUE", True),
+    ("y", True),
+    ("yes", True),
+    (0, False),
+    (1, True),
+    (False, False),
+    (True, True),
+]
 
 
-def test_settings_defaults() -> None:
-    """Ensure the settings defaults are set up correctly."""
-    s = make_settings()
-    assert s.destination == "local_fs"
-    assert s.start_at == 0
-    assert s.output is None
-    assert s.input_dir == INPUT_MOUNT
+# Generic settings tests
+@pytest.mark.parametrize(
+    ("settings_cls", "args", "expected"),
+    [
+        # default values
+        (CtsSettings, {}, DEFAULT_CTS_SETTINGS_RECONCILED),
+        (BatchedFileInputSettings, {}, DEFAULT_BATCH_FILE_SETTINGS_RECONCILED),
+        # all args specified
+        (CtsSettings, TEST_CTS_SETTINGS, TEST_CTS_SETTINGS_RECONCILED),
+        (BatchedFileInputSettings, TEST_BATCH_FILE_SETTINGS, TEST_BATCH_FILE_SETTINGS_RECONCILED),
+    ],
+)
+def test_settings_all_settings_specified(
+    dlt_config: dict[str, Any], settings_cls: type[CtsSettings], args: dict[str, Any], expected: dict[str, Any]
+) -> None:
+    """Ensure the CTS settings are set up correctly."""
+    s = make_settings(settings_cls, dlt_config=dlt_config, **args)
+    check_settings(s, dict(expected))
 
 
-def test_settings_all_params_set() -> None:
-    """Ensure that settings are set correctly when all args are specified."""
-    s = make_settings(
-        input_dir="/dir/path",
-        destination=VALID_DESTINATIONS[0],
-        start_at=START_AT_STRING,
-        output="/some/dir",
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_cli_app_run_default_settings(settings_cls: type[CtsSettings], dlt_config: dict[str, Any]) -> None:
+    """Ensure the CTS settings are set up correctly, CLI version."""
+    s = CliApp.run(settings_cls, dlt_config=dlt_config)
+    expected = (
+        DEFAULT_CTS_SETTINGS_RECONCILED if settings_cls == CtsSettings else DEFAULT_BATCH_FILE_SETTINGS_RECONCILED
     )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
+    check_settings(s, dict(expected))
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_settings_no_dlt_config_error(settings_cls: type[CtsSettings]) -> None:
+    """Ensure an error is raised if there is no dlt_config."""
+    with pytest.raises(ValidationError, match=r"dlt_config must be defined"):
+        make_settings(settings_cls, dlt_config=None)
+
+
+@pytest.mark.parametrize("invalid_destination_config", [{}, {"destination": {}}])
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_settings_no_destinations_set(
+    settings_cls: type[CtsSettings], invalid_destination_config: dict[str, dict[Any, Any]]
+) -> None:
+    """Ensure that destinations are specified in the dlt config."""
+    with pytest.raises(ValueError, match="No valid destinations found in dlt configuration"):
+        make_settings(settings_cls, dlt_config=invalid_destination_config)
+
+
+# same thing but via CliApp.run
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize(
+    ("dlt_config", "error", "err_msg"),
+    [
+        (None, ValidationError, "dlt_config must be defined"),
+        ({}, ValueError, "No valid destinations found in dlt configuration"),
+        ({"destination": {}}, ValueError, "No valid destinations found in dlt configuration"),
+    ],
+)
+def test_cli_app_run_dlt_config_errors(
+    settings_cls: type[CtsSettings], dlt_config: None | dict[str, Any], error: type[Exception], err_msg: str
+) -> None:
+    """Test all the variants of the Settings fields."""
+    with pytest.raises(error, match=err_msg):
+        CliApp.run(settings_cls, dlt_config=dlt_config)
 
 
-@pytest.mark.parametrize("destination", VALID_DESTINATIONS)
-def test_settings_valid_variants_accepted(destination: str) -> None:
-    """Ensure that each valid uniprot_kb_variant value is accepted without error."""
-    s = make_settings(destination=destination)
-    assert s.destination == destination
+# destination tests
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+def test_settings_valid_destinations_accepted(
+    use_destination: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Test valid destinations against the settings class."""
+    s = make_settings(settings_cls, dlt_config=dlt_config, use_destination=use_destination)
+    assert s.use_destination == use_destination
 
 
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_invalid_destination_raises(bad: str) -> None:
-    """Ensure that an unrecognised destination raises a ValidationError."""
-    with pytest.raises(ValidationError, match="destination must be one of"):
-        make_settings(destination=bad)
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", INVALID_DESTINATIONS)
+def test_settings_invalid_destination_raises(
+    use_destination: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that an unrecognised use_destination raises a ValidationError."""
+    with pytest.raises(ValidationError, match=r"use_destination must be one of \['local_fs', 's3'\]"):
+        make_settings(settings_cls, dlt_config=dlt_config, use_destination=use_destination)
 
 
-def _cliapp_run(cli_args: list[str]) -> BatchedFileInputSettings:
-    """Tests that Settings correctly parses command-line arguments via CliApp.
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_settings_destination_has_no_bucket_url(settings_cls: type[CtsSettings]) -> None:
+    """Ensure that destinations have a bucket_url."""
+    with pytest.raises(ValueError, match="No bucket_url specified for destination local_fs"):
+        make_settings(settings_cls, dlt_config={"destination": {"local_fs": None}}, use_destination="local_fs")
 
-    Uses CliApp.run with explicit cli_args to avoid mutating sys.argv globally.
-    """
-    return CliApp.run(BatchedFileInputSettings, cli_args=cli_args)
 
+# destination tests, CLI versions
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+@pytest.mark.parametrize("destination_arg", ARG_ALIASES["use_destination"])
+def test_cli_app_run_valid_destinations_accepted(
+    use_destination: str, settings_cls: type[CtsSettings], destination_arg: str, dlt_config: dict[str, Any]
+) -> None:
+    """Test valid destinations using the command line."""
+    s = CliApp.run(settings_cls, dlt_config=dlt_config, cli_args=[destination_arg, use_destination])
+    assert s.use_destination == use_destination
 
-@pytest.mark.parametrize("input_dir", ["-i", "--input-dir", "--input_dir"])
-@pytest.mark.parametrize("destination", ["-d", "--destination"])
-@pytest.mark.parametrize("start_at", ["-s", "--start-at", "--start_at"])
-@pytest.mark.parametrize("output", ["-o", "--output"])
-def test_cli_all_variants(input_dir: str, destination: str, start_at: str, output: str) -> None:
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", INVALID_DESTINATIONS)
+@pytest.mark.parametrize("destination_arg", ARG_ALIASES["use_destination"])
+def test_cli_app_run_invalid_destinations_raises(
+    use_destination: str, settings_cls: type[CtsSettings], destination_arg: str, dlt_config: dict[str, Any]
+) -> None:
+    """Test invalid destinations using the command line."""
+    with pytest.raises(ValidationError, match="use_destination must be one of"):
+        CliApp.run(settings_cls, dlt_config=dlt_config, cli_args=[destination_arg, use_destination])
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("destination_arg", ARG_ALIASES["use_destination"])
+def test_cli_app_run_destination_has_no_bucket_url(settings_cls: type[CtsSettings], destination_arg: str) -> None:
+    """Ensure that destinations have a bucket_url."""
+    with pytest.raises(ValueError, match="No bucket_url specified for destination local_fs"):
+        CliApp.run(settings_cls, dlt_config={"destination": {"local_fs": None}}, cli_args=[destination_arg, "local_fs"])
+
+
+# boolean fields
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize(("input_arg", "value"), TRUE_FALSE_VALUES)
+@pytest.mark.parametrize("input_arg_name", ["use_output_dir_for_pipeline_metadata", "dev_mode"])
+def test_settings_boolean_variants_accepted(
+    input_arg: str, value: bool, input_arg_name: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that each valid boolean value is accepted without error."""
+    s = make_settings(settings_cls, dlt_config=dlt_config, **{input_arg_name: input_arg})  # type: ignore[reportArgumentType]
+    assert getattr(s, input_arg_name) == value
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("value", INVALID_BOOLEAN_VALUES)
+@pytest.mark.parametrize("input_arg_name", ["use_output_dir_for_pipeline_metadata", "dev_mode"])
+def test_settings_invalid_boolean_variants_raises(
+    value: bool, input_arg_name: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that each invalid boolean value is throws an error."""
+    with pytest.raises(ValidationError, match="Input should be a valid boolean"):
+        make_settings(settings_cls, dlt_config=dlt_config, **{input_arg_name: value})  # type: ignore[reportArgumentType]
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize(("input_arg", "value"), TRUE_FALSE_VALUES)
+@pytest.mark.parametrize("input_arg_name", ["use_output_dir_for_pipeline_metadata", "dev_mode"])
+def test_cli_app_run_boolean_variants_accepted(
+    input_arg: str, value: bool, input_arg_name: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that each invalid boolean value is throws an error."""
+    s = CliApp.run(settings_cls, dlt_config=dlt_config, cli_args=[input_arg_name, str(input_arg)])
+    if input_arg_name in ARG_ALIASES["use_output_dir_for_pipeline_metadata"]:
+        assert s.use_output_dir_for_pipeline_metadata == value
+    elif input_arg_name in ARG_ALIASES["dev_mode"]:
+        assert s.dev_mode == value
+
+
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("value", INVALID_BOOLEAN_VALUES)
+@pytest.mark.parametrize(
+    "input_arg_name", [*ARG_ALIASES["use_output_dir_for_pipeline_metadata"], *ARG_ALIASES["dev_mode"]]
+)
+def test_cli_app_run_invalid_boolean_values_raises(
+    value: bool, input_arg_name: str, settings_cls: type[CtsSettings], dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that each invalid boolean value is throws an error."""
+    with pytest.raises(ValidationError, match="Input should be a valid boolean"):
+        CliApp.run(settings_cls, dlt_config=dlt_config, cli_args=[input_arg_name, str(value)])
+
+
+# input and output path coercion
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize(
+    ("raw", "expected"),
+    [
+        ("/some/path/", "/some/path"),
+        ("/some/path//", "/some/path"),
+        ("/some/path", "/some/path"),
+        ("/", "/"),
+        ("", ""),
+    ],
+)
+@pytest.mark.parametrize("field_name", ["input_dir", "output"])
+def test_settings_trailing_slash_stripped(
+    settings_cls: type[CtsSettings],
+    raw: str,
+    expected: str,
+    field_name: str,
+    dlt_config: dict[str, Any],
+) -> None:
+    """Ensure that validate_dir_path removes trailing slashes but leaves directory slashes intact."""
+    s = make_settings(settings_cls, dlt_config=dlt_config, **{field_name: raw})
+    # output gets filled in with the default if it is falsy
+    if field_name == "output" and raw == "":
+        expected = "/output_dir"
+    assert getattr(s, field_name) == expected
+
+
+# All arguments set, using CliApp.run
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("dev_mode", ARG_ALIASES["dev_mode"])
+@pytest.mark.parametrize("input_dir", ARG_ALIASES["input_dir"])
+@pytest.mark.parametrize("output", ARG_ALIASES["output"])
+@pytest.mark.parametrize("start_at", ARG_ALIASES["start_at"])
+@pytest.mark.parametrize("use_destination", ARG_ALIASES["use_destination"])
+@pytest.mark.parametrize(
+    "use_output_dir_for_pipeline_metadata",
+    ARG_ALIASES["use_output_dir_for_pipeline_metadata"],
+)
+def test_cli_app_run_alt_settings(  # noqa: PLR0913
+    settings_cls: type[CtsSettings],
+    dev_mode: str,
+    input_dir: str,
+    output: str,
+    start_at: str,
+    use_destination: str,
+    use_output_dir_for_pipeline_metadata: str,
+    dlt_config: dict[str, Any],
+) -> None:
     """Test all the variants of the Settings fields."""
-    s = _cliapp_run(
-        [
-            input_dir,
-            "/dir/path",
-            destination,
-            VALID_DESTINATIONS[0],
-            start_at,
-            START_AT_STRING,
-            output,
-            "/some/dir",
-        ]
+    # TEST_BATCH_FILE_SETTINGS is identical to TEST_CTS_SETTINGS, but also includes start_at
+    cli_args = [
+        dev_mode,
+        TEST_BATCH_FILE_SETTINGS["dev_mode"],
+        input_dir,
+        TEST_BATCH_FILE_SETTINGS["input_dir"],
+        output,
+        TEST_BATCH_FILE_SETTINGS["output"],
+        use_destination,
+        TEST_BATCH_FILE_SETTINGS["use_destination"],
+        use_output_dir_for_pipeline_metadata,
+        TEST_BATCH_FILE_SETTINGS["use_output_dir_for_pipeline_metadata"],
+    ]
+    # add in start_at for the BatchedFileInputSettings
+    if settings_cls == BatchedFileInputSettings:
+        cli_args.extend([start_at, TEST_BATCH_FILE_SETTINGS["start_at"]])
+
+    expected = TEST_CTS_SETTINGS_RECONCILED if settings_cls == CtsSettings else TEST_BATCH_FILE_SETTINGS_RECONCILED
+
+    s = CliApp.run(
+        settings_cls,
+        dlt_config=dlt_config,
+        cli_args=cli_args,
+    )
+    check_settings(s, expected)
+
+
+# CLI App: ignore extra properties
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+def test_cli_app_run_invalid_params_ignored(settings_cls: type[CtsSettings], dlt_config: dict[str, Any]) -> None:
+    """Test that invalid parameter values are ignored."""
+    s = CliApp.run(
+        settings_cls,
+        dlt_config=dlt_config,
+        cli_args=[
+            "--some_random_arg",
+            "some value",
+            "-q",
+            "answer",
+        ],
     )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
+    output = s.model_dump()
+
+    assert "some value" not in output.values()
+    assert "answer" not in output.values()
+
+
+# values set during reconcile_with_dlt_config
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+def test_settings_reconcile_with_dlt_config_output_resolved_from_dlt_config_bucket_url(
+    settings_cls: type[CtsSettings],
+    use_destination: str,
+    dlt_config: dict[str, Any],
+) -> None:
+    """When output is empty, it is populated from dlt config's bucket_url."""
+    s = make_settings(
+        settings_cls,
+        dlt_config=dlt_config,
+        output="",
+        use_destination=use_destination,
+    )
+    assert s.output == dlt_config[f"destination.{use_destination}.bucket_url"]
+
+
+# properties derived from self.output
+@pytest.mark.parametrize("settings_cls", SETTINGS_CLASSES)
+@pytest.mark.parametrize("output", ["", "/output/dir", "some/convoluted/path/to/dir/"])
+@pytest.mark.parametrize("use_output_dir_for_pipeline_metadata", [True, False])
+@pytest.mark.parametrize("use_destination", VALID_DESTINATIONS)
+def test_settings_generate_pipeline_raw_data_dirs(
+    settings_cls: type[CtsSettings],
+    output: str,
+    use_output_dir_for_pipeline_metadata: bool,
+    dlt_config: dict[str, Any],
+    use_destination: str,
+) -> None:
+    """Ensure that the correct paths are generated for pipeline and raw data directories."""
+    s = make_settings(
+        settings_cls,
+        dlt_config=dlt_config,
+        output=output,
+        use_destination=use_destination,
+        use_output_dir_for_pipeline_metadata=use_output_dir_for_pipeline_metadata,
+    )
+
+    expected = {
+        **DEFAULT_CTS_SETTINGS_RECONCILED,
+        "use_destination": use_destination,
+        "use_output_dir_for_pipeline_metadata": use_output_dir_for_pipeline_metadata,
+        "output": output.rstrip("/") or dlt_config[f"destination.{use_destination}.bucket_url"],
+    }
+
+    if settings_cls == BatchedFileInputSettings:
+        expected["start_at"] = DEFAULT_START_AT
+
+    # list containing the projected raw_data_dir and pipeline_dir
+    expected_properties = {
+        "": [str(Path(expected["output"]) / "raw_data"), str(Path(expected["output"]) / ".dlt_conf")],
+        "/output/dir": [str(Path("/output/dir") / "raw_data"), str(Path("/output/dir") / ".dlt_conf")],
+        "some/convoluted/path/to/dir/": [
+            str(Path("some/convoluted/path/to/dir") / "raw_data"),
+            str(Path("some/convoluted/path/to/dir") / ".dlt_conf"),
+        ],
+    }
 
+    expected["raw_data_dir"] = expected_properties[output][0]
+    expected["pipeline_dir"] = expected_properties[output][1] if use_output_dir_for_pipeline_metadata else None
 
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_cli_invalid_destination_via_cli_raises(bad: str) -> None:
-    """Ensure that an invalid destination passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match="Value error, destination must be one of"):
-        _cliapp_run(["--destination", bad])
+    check_settings(s, expected)
diff --git a/tests/pipelines/test_ncbi_rest_api.py b/tests/pipelines/test_ncbi_rest_api.py
index 64cb9175..a5029f3a 100644
--- a/tests/pipelines/test_ncbi_rest_api.py
+++ b/tests/pipelines/test_ncbi_rest_api.py
@@ -6,18 +6,23 @@
 from unittest.mock import MagicMock, patch
 
 import pytest
+from dlt.extract.items import DataItemWithMeta
+from frozendict import frozendict
 from pydantic import ValidationError
 from pydantic_settings import CliApp
 from requests import HTTPError
 
+from cdm_data_loaders.pipelines import core
 from cdm_data_loaders.pipelines import ncbi_rest_api as ncbi_module
-from cdm_data_loaders.pipelines.cts_defaults import INPUT_MOUNT, OUTPUT_MOUNT, VALID_DESTINATIONS
+from cdm_data_loaders.pipelines.cts_defaults import ARG_ALIASES
 from cdm_data_loaders.pipelines.ncbi_rest_api import (
     ANNOTATION,
+    ARG_ALIAS_BATCH_SIZE,
     DATASET,
     DATASET_NAME,
     ERROR,
-    Settings,
+    NcbiSettings,
+    assemble_assembly_reports,
     assembly_list,
     cli,
     get_annotation_report,
@@ -25,13 +30,19 @@
     get_dataset_reports,
     run_ncbi_pipeline,
 )
+from tests.pipelines.conftest import (
+    DEFAULT_VCR_CONFIG,
+    TEST_CTS_SETTINGS,
+    TEST_CTS_SETTINGS_RECONCILED,
+    check_settings,
+    make_settings_autofill_config,
+)
 
-CASSETTES_DIR = "tests/cassettes"
 
-DLT_TESTING_CONFIG = {
-    "destination.local_fs.bucket_url": "tests/dlt_test_output",
-    "normalize.data_writer.disable_compression": True,
-}
+@pytest.fixture(autouse=True)
+def patch_dlt_config(dlt_config: dict[str, Any], monkeypatch: pytest.MonkeyPatch) -> None:
+    """Monkeypatch the dlt config in all tests."""
+    monkeypatch.setattr(core.dlt, "config", dlt_config)
 
 
 @pytest.fixture(autouse=True)
@@ -40,23 +51,29 @@ def patch_rest_client_hooks(monkeypatch: pytest.MonkeyPatch) -> None:
     monkeypatch.setattr("cdm_data_loaders.pipelines.ncbi_rest_api.REST_CLIENT_HOOKS", {})
 
 
+BATCH_SIZE_STRING = "500"
+BATCH_SIZE_INT = 500
+
+TEST_NCBI_SETTINGS = frozendict(
+    **TEST_CTS_SETTINGS,
+    batch_size=BATCH_SIZE_STRING,
+)
+
+TEST_NCBI_SETTINGS_RECONCILED = frozendict(
+    **TEST_CTS_SETTINGS_RECONCILED,
+    batch_size=BATCH_SIZE_INT,
+)
+
+
 @pytest.fixture(scope="module")
 def vcr_config() -> dict[str, Any]:
     """VCR config for tests that make HTTP requests."""
-    return {
-        "cassette_library_dir": CASSETTES_DIR,
-        "record_mode": "once",  # record on first run, replay thereafter
-        "serializer": "yaml",
-        "match_on": ["method", "scheme", "host", "path", "query"],
-        # strip the NCBI API key from cassettes
-        "filter_query_parameters": ["api_key"],
-        "filter_headers": ["api_key"],
-        "decode_compressed_response": True,
-    }
+    return {**DEFAULT_VCR_CONFIG}
 
 
 ID_WITH_2K_ANNOTS = "GCF_000003135.1"
 ID_WITH_500_ANNOTS = "GCF_000007725.1"
+ID_TRIGGERS_500_ERR = "GCF_500_ERROR"
 VALID_IDS = [ID_WITH_500_ANNOTS, ID_WITH_2K_ANNOTS]
 INVALID_ID = "invalid_id"
 ALL_IDS = [*VALID_IDS, INVALID_ID]
@@ -64,12 +81,6 @@ def vcr_config() -> dict[str, Any]:
 BATCH_SIZE_STRING = "500"
 
 
-@pytest.fixture(scope="module")
-def config() -> Settings:
-    """Default config for testing."""
-    return Settings.model_validate({"input_dir": "/fake/dir"})
-
-
 @pytest.fixture(scope="module")
 def valid_assembly_ids() -> list[str]:
     """A list of assembly IDs."""
@@ -94,103 +105,9 @@ def assembly_ids(valid_assembly_ids: list[str], invalid_assembly_id: str) -> lis
     return [*valid_assembly_ids, invalid_assembly_id]
 
 
-def make_settings(**kwargs: str | int | bool) -> Settings:
-    """Generate a validated Settings object."""
-    return Settings.model_validate(kwargs)
-
-
-def test_settings_defaults() -> None:
-    """Ensure the settings defaults are set up correctly."""
-    s = make_settings()
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.dev_mode is False
-    assert s.input_dir == INPUT_MOUNT
-    assert s.pipeline_dir is None
-    # FIXME: should be dlt.config["destination.local_fs.bucket_url"]
-    assert s.output == OUTPUT_MOUNT
-    assert s.use_output_dir_for_pipeline_metadata is False
-    assert s.batch_size == ncbi_module.MAX_RESULTS_PER_PAGE
-
-
-def test_settings_all_params_set() -> None:
-    """Ensure that settings are set correctly when all args are specified."""
-    s = make_settings(
-        destination=VALID_DESTINATIONS[0],
-        dev_mode=True,
-        input_dir="/dir/path",
-        output="/some/dir",
-        use_output_dir_for_pipeline_metadata=True,
-        batch_size=BATCH_SIZE,
-    )
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.dev_mode is True
-    assert s.input_dir == "/dir/path"
-    assert s.pipeline_dir == Path("/some") / "dir" / ".dlt_conf"
-    assert s.output == "/some/dir"
-    assert s.use_output_dir_for_pipeline_metadata is True
-    assert s.batch_size == BATCH_SIZE
-
-
-@pytest.mark.parametrize("destination", VALID_DESTINATIONS)
-def test_settings_valid_variants_accepted(destination: str) -> None:
-    """Ensure that each valid destination value is accepted without error."""
-    s = make_settings(destination=destination)
-    assert s.destination == destination
-
-
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_invalid_destination_raises(bad: str) -> None:
-    """Ensure that an unrecognised destination raises a ValidationError."""
-    with pytest.raises(ValidationError, match="destination must be one of"):
-        make_settings(destination=bad)
-
-
-@pytest.mark.parametrize("input_dir", ["-i", "--input-dir", "--input_dir"])
-@pytest.mark.parametrize("destination", ["-d", "--destination"])
-@pytest.mark.parametrize("use_output_dir_for_pipeline_metadata", ["-p", "--pipeline-dir", "--pipeline_dir"])
-@pytest.mark.parametrize("output", ["-o", "--output"])
-@pytest.mark.parametrize("dev_mode_flag", ["--dev", "--dev-mode", "--dev_mode"])
-@pytest.mark.parametrize("batch_size", ["-b", "--batch-size", "--batch_size"])
-def test_cli_all_variants(  # noqa: PLR0913
-    input_dir: str,
-    destination: str,
-    use_output_dir_for_pipeline_metadata: str,
-    output: str,
-    dev_mode_flag: str,
-    batch_size: str,
-) -> None:
-    """Test all the variants of the Settings fields."""
-    s = CliApp.run(
-        Settings,
-        [
-            input_dir,
-            "/dir/path",
-            destination,
-            VALID_DESTINATIONS[0],
-            output,
-            "/some/dir",
-            use_output_dir_for_pipeline_metadata,
-            "True",
-            dev_mode_flag,
-            "True",
-            batch_size,
-            BATCH_SIZE_STRING,
-        ],
-    )
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.dev_mode is True
-    assert s.input_dir == "/dir/path"
-    assert s.pipeline_dir == Path("/some") / "dir" / ".dlt_conf"
-    assert s.output == "/some/dir"
-    assert s.use_output_dir_for_pipeline_metadata is True
-    assert s.batch_size == BATCH_SIZE
-
-
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_cli_invalid_destination_via_cli_raises(bad: str) -> None:
-    """Ensure that an invalid destination passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match="Value error, destination must be one of"):
-        CliApp.run(Settings, cli_args=["--destination", bad])
+def make_settings(**kwargs: str | int | bool) -> NcbiSettings:
+    """Generate a validated NcbiSettings object."""
+    return NcbiSettings.model_validate(kwargs)
 
 
 @pytest.mark.parametrize(
@@ -203,68 +120,84 @@ def test_cli_invalid_destination_via_cli_raises(bad: str) -> None:
         ("", "Input should be a valid integer"),
     ],
 )
-def test_cli_invalid_batch_size_via_cli_raises(bad_batch_size: str, message: str) -> None:
+@pytest.mark.parametrize("use_cliapp", [True, False])
+def test_cli_invalid_batch_size_via_cli_raises(bad_batch_size: str, message: str, use_cliapp: bool) -> None:
     """Ensure that an invalid batch size passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match=message):
-        CliApp.run(Settings, cli_args=["--batch-size", bad_batch_size])
+    if use_cliapp:
+        with pytest.raises(ValidationError, match=message):
+            CliApp.run(NcbiSettings, cli_args=["--batch-size", bad_batch_size])
+    else:
+        with pytest.raises(ValidationError, match=message):
+            make_settings_autofill_config(NcbiSettings, batch_size=bad_batch_size)
+
+
+def test_settings_all_params_set() -> None:
+    """Ensure that settings are set correctly when all args are specified."""
+    s = make_settings_autofill_config(NcbiSettings, **TEST_NCBI_SETTINGS)
+    check_settings(s, TEST_NCBI_SETTINGS_RECONCILED)
 
 
+@pytest.mark.parametrize("batch_size", ARG_ALIAS_BATCH_SIZE)
+@pytest.mark.parametrize("dev_mode", ARG_ALIASES["dev_mode"])
+@pytest.mark.parametrize("input_dir", ARG_ALIASES["input_dir"])
+@pytest.mark.parametrize("output", ARG_ALIASES["output"])
+@pytest.mark.parametrize("use_destination", ARG_ALIASES["use_destination"])
 @pytest.mark.parametrize(
-    ("boolean", "valid", "value"),
-    [
-        (None, False, None),
-        ("notaboolean", False, None),
-        ("123", False, None),
-        ("", False, None),
-        ("Truee", False, None),
-        ("Falsee", False, None),
-        ("true", True, True),
-        ("false", True, False),
-        ("True", True, True),
-        ("False", True, False),
-        ("1", True, True),
-        ("0", True, False),
-    ],
+    "use_output_dir_for_pipeline_metadata",
+    ARG_ALIASES["use_output_dir_for_pipeline_metadata"],
 )
-def test_cli_invalid_boolean_via_cli_raises(boolean: str, valid: bool, value: bool) -> None:
-    """Ensure that an invalid boolean passed via CLI causes a ValidationError.
-
-    :param boolean: the value of the boolean
-    :type boolean: str
-    :param valid: whether or not this is a valid CLI value for a boolean field
-    :type valid: bool
-    :param value: the expected parsed value of the boolean
-    :type value: bool
-    """
-    if not valid:
-        with pytest.raises(ValidationError, match="Input should be a valid boolean, unable to interpret input"):
-            CliApp.run(Settings, cli_args=["--dev-mode", boolean])
-    else:
-        s = CliApp.run(Settings, cli_args=["--dev-mode", boolean])
-        assert s.dev_mode is value
+def test_cli_all_variants(  # noqa: PLR0913
+    batch_size: str,
+    dev_mode: str,
+    input_dir: str,
+    output: str,
+    use_destination: str,
+    use_output_dir_for_pipeline_metadata: str,
+    dlt_config: dict[str, Any],
+) -> None:
+    """Test all the variants of the NcbiSettings fields."""
+    s = CliApp.run(
+        NcbiSettings,
+        dlt_config=dlt_config,
+        cli_args=[
+            batch_size,
+            BATCH_SIZE_STRING,
+            dev_mode,
+            TEST_NCBI_SETTINGS["dev_mode"],
+            input_dir,
+            TEST_NCBI_SETTINGS["input_dir"],
+            output,
+            TEST_NCBI_SETTINGS["output"],
+            use_destination,
+            TEST_NCBI_SETTINGS["use_destination"],
+            use_output_dir_for_pipeline_metadata,
+            TEST_NCBI_SETTINGS["use_output_dir_for_pipeline_metadata"],
+        ],
+    )
+    check_settings(s, TEST_NCBI_SETTINGS_RECONCILED)
 
 
 def test_cli_passes_settings_class_to_run_cli() -> None:
-    """Ensure that cli() calls run_cli with Settings as the settings class."""
+    """Ensure that cli() calls run_cli with NcbiSettings as the settings class."""
     with patch.object(ncbi_module, "run_cli") as mock_run_cli:
         cli()
 
     mock_run_cli.assert_called_once()
-    assert mock_run_cli.call_args[0] == (Settings, run_ncbi_pipeline)
+    assert mock_run_cli.call_args[0] == (NcbiSettings, run_ncbi_pipeline)
 
 
-def test_cli_calls_run_ncbi_pipeline(monkeypatch: pytest.MonkeyPatch) -> None:
-    """Ensure that cli() calls run_ncbi_pipeline with the config."""
-    mock_settings_instance = MagicMock(spec=Settings)
+def test_cli_calls_run_ncbi_pipeline(monkeypatch: pytest.MonkeyPatch, dlt_config: dict[str, Any]) -> None:
+    """Ensure that cli() calls run_ncbi_pipeline with the settings."""
+    mock_settings_instance = MagicMock()
     mock_settings_cls = MagicMock(return_value=mock_settings_instance)
     mock_run_ncbi_pipeline = MagicMock()
 
-    monkeypatch.setattr(ncbi_module, "Settings", mock_settings_cls)
+    monkeypatch.setattr(ncbi_module, "NcbiSettings", mock_settings_cls)
     monkeypatch.setattr(ncbi_module, "run_ncbi_pipeline", mock_run_ncbi_pipeline)
 
     cli()
 
-    mock_settings_cls.assert_called_once_with()
+    mock_settings_cls.assert_called_once_with(dlt_config=dlt_config)
     mock_run_ncbi_pipeline.assert_called_once_with(mock_settings_instance)
 
 
@@ -290,9 +223,9 @@ def check_annotation_report(annotation_report: list[dict[str, Any]] | None, asse
 
 def test_assembly_list_resource() -> None:
     """Test that the assembly list resource yields the expected assembly IDs."""
-    config = Settings.model_validate({"input_dir": "tests/data/ncbi_rest_api/input"})
+    settings: NcbiSettings = make_settings_autofill_config(NcbiSettings, input_dir="tests/data/ncbi_rest_api/input")  # type: ignore[reportAssignmentType]
 
-    ass_list = list(assembly_list(config))
+    ass_list = list(assembly_list(settings))
     assert ass_list == [
         "GCF_029958545.3",
         "GCF_029958565.3",
@@ -308,7 +241,6 @@ def test_assembly_list_resource() -> None:
 @pytest.mark.parametrize("dev_mode", [False, True, None])
 @pytest.mark.parametrize("use_pipeline_dir", [False, True, None])
 def test_run_ncbi_pipeline_sets_core_run_pipeline_args_correctly(
-    config: Settings,
     dev_mode: bool | None,
     use_pipeline_dir: bool | None,
     mock_dlt: MagicMock,
@@ -326,22 +258,40 @@ def test_run_ncbi_pipeline_sets_core_run_pipeline_args_correctly(
     if use_pipeline_dir is not None:
         base_settings["use_output_dir_for_pipeline_metadata"] = use_pipeline_dir
 
-    config = Settings.model_validate(base_settings)
+    settings: NcbiSettings = make_settings_autofill_config(NcbiSettings, **base_settings)  # type: ignore[reportAssignmentType]
+
+    check_settings(
+        settings,
+        {
+            "dev_mode": bool(dev_mode),
+            "input_dir": "tests/data/ncbi_rest_api/input",
+            "output": "/some/dir",
+            "pipeline_dir": "/some/dir/.dlt_conf" if use_pipeline_dir else None,
+            "raw_data_dir": "/some/dir/raw_data",
+            "use_destination": "local_fs",
+            "use_output_dir_for_pipeline_metadata": bool(use_pipeline_dir),
+            "batch_size": 1000,
+        },
+    )
+
+    run_ncbi_pipeline(settings)
 
-    run_ncbi_pipeline(config)
+    mock_dlt.destination.assert_called_once_with(settings.use_destination, max_table_nesting=0)
+    mock_dlt.destination.assert_called_once()
+    assert mock_dlt.destination.call_args_list[0].kwargs == {"max_table_nesting": 0}
+    assert mock_dlt.destination.call_args_list[0].args == ("local_fs",)
+    mock_assembly_list.bind.assert_called_once_with(settings)
 
-    mock_dlt.destination.assert_called_once_with(config.destination, max_table_nesting=0)
     mock_dlt.pipeline.assert_called_once()
-    mock_assembly_list.bind.assert_called_once_with(config)
     assert mock_dlt.pipeline.call_args.kwargs["destination"] == mock_dlt.destination.return_value
     assert mock_dlt.pipeline.call_args.kwargs["pipeline_name"] == DATASET_NAME
     assert mock_dlt.pipeline.call_args.kwargs["dataset_name"] == DATASET_NAME
     if dev_mode:  # truthy
         assert mock_dlt.pipeline.call_args.kwargs["dev_mode"] is True
     else:
-        assert mock_dlt.pipeline.call_args.kwargs["dev_mode"] is False
+        assert "dev_mode" not in mock_dlt.pipeline.call_args.kwargs
     if use_pipeline_dir:  # truthy
-        assert mock_dlt.pipeline.call_args.kwargs["pipelines_dir"] == Path(config.output) / ".dlt_conf"  # type: ignore[reportArgumentType]
+        assert mock_dlt.pipeline.call_args.kwargs["pipelines_dir"] == f"{settings.output}/.dlt_conf"  # type: ignore[reportArgumentType]
     else:
         assert "pipelines_dir" not in mock_dlt.pipeline.call_args.kwargs
 
@@ -386,7 +336,7 @@ def test_get_annotation_report_multi_page() -> None:
 def test_get_annotation_report_multi_page_err() -> None:
     """An error in the middle of a multi-page retrieval should stop the whole retrieval process."""
     with pytest.raises(HTTPError, match="500 Server Error: Internal Server Error for url"):
-        get_annotation_report(ID_WITH_2K_ANNOTS)
+        get_annotation_report(ID_TRIGGERS_500_ERR)
 
 
 @pytest.mark.default_cassette("test_get_assembly_reports.yaml")
@@ -415,12 +365,77 @@ def test_get_assembly_reports() -> None:
     assert assembly_reports[ERROR] == []
 
 
+RECORDED_ERRORS = {
+    "dataset_404": {
+        "assembly_id": None,
+        "assembly_id_list": ALL_IDS,
+        "error_class": "HTTPError",
+        "error_from": "dataset_report",
+        "message": '404 Client Error: Not Found for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000\nResponse: {"error":"Not Found","code":404,"message":"Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
+        "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000",
+        "status": 404,
+        "reason": "Not Found",
+    },
+    "annotation_report_500": {
+        "assembly_id": ID_WITH_2K_ANNOTS,
+        "assembly_id_list": None,
+        "error_class": "HTTPError",
+        "error_from": "annotation_report",
+        "message": '500 Server Error: Internal Server Error for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw\nResponse: {"error":"Internal Server Error","code":500,"message":"Internal Server Error (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
+        "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw",
+        "status": 500,
+        "reason": "Internal Server Error",
+    },
+    "annotation_report_404": {
+        "assembly_id": ID_WITH_500_ANNOTS,
+        "assembly_id_list": None,
+        "error_class": "HTTPError",
+        "error_from": "annotation_report",
+        "message": '404 Client Error: Not Found for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1/annotation_report?page_size=1000\nResponse: {"error":"Not Found","code":404,"message":"Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
+        "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1/annotation_report?page_size=1000",
+        "status": 404,
+        "reason": "Not Found",
+    },
+    "value_error": {
+        "assembly_id": INVALID_ID,
+        "assembly_id_list": None,
+        "error_class": "ValueError",
+        "error_from": "annotation_report",
+        "message": f"Some error message involving {INVALID_ID}.",
+        "request_url": None,
+        "status": None,
+        "reason": None,
+    },
+}
+
+
 @mock.patch("tenacity.nap.time.sleep", MagicMock())
 @pytest.mark.default_cassette("test_get_assembly_reports_annotation_report_errors.yaml")
 @pytest.mark.vcr
 def test_get_assembly_reports_annotation_report_errors() -> None:
     """Test the retrieval of assembly data when errors occur fetching annotation reports."""
-    assembly_reports = get_assembly_reports(ALL_IDS)
+    original_get_annotation_report = get_annotation_report
+
+    def patched_get_annotation_report(assembly_id: str) -> list[dict[str, Any]] | None:
+        """Patched version of get_annotation_report that throws a value error with a certain input.
+
+        :param assembly_id: assembly ID
+        :type assembly_id: str
+        :raises ValueError: if the ID is INVALID_ID
+        :return: output from the real get_annotation_report
+        :rtype: list[dict[str, Any]] | None
+        """
+        if assembly_id == INVALID_ID:
+            err_msg = f"Some error message involving {INVALID_ID}."
+            raise ValueError(err_msg)
+        return original_get_annotation_report(assembly_id)
+
+    with mock.patch(
+        "cdm_data_loaders.pipelines.ncbi_rest_api.get_annotation_report",
+        side_effect=patched_get_annotation_report,
+    ):
+        assembly_reports = get_assembly_reports(ALL_IDS)
+
     assert set(assembly_reports) == {DATASET, ANNOTATION, ERROR}
     for datatype in [DATASET, ANNOTATION]:
         assert set(assembly_reports[datatype]) == set(ALL_IDS)
@@ -431,18 +446,7 @@ def test_get_assembly_reports_annotation_report_errors() -> None:
     check_annotation_report(assembly_reports[ANNOTATION][ID_WITH_500_ANNOTS], ID_WITH_500_ANNOTS)
     assert assembly_reports[ANNOTATION][ID_WITH_2K_ANNOTS] is None
 
-    assert assembly_reports[ERROR] == [
-        {
-            "assembly_id": ID_WITH_2K_ANNOTS,
-            "assembly_id_list": None,
-            "error_class": "HTTPError",
-            "error_from": "annotation_report",
-            "message": '500 Server Error: Internal Server Error for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw\nResponse: {"error":"Internal Server Error","code":500,"message":"Internal Server Error (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/) (1D3311AB4E92F955000055F41870A1E3.1.1)"}\n',
-            "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw",
-            "status": 500,
-            "reason": "Internal Server Error",
-        }
-    ]
+    assert assembly_reports[ERROR] == [RECORDED_ERRORS["annotation_report_500"], RECORDED_ERRORS["value_error"]]
 
 
 @mock.patch("tenacity.nap.time.sleep", MagicMock())
@@ -458,60 +462,43 @@ def test_get_assembly_reports_dataset_report_errors() -> None:
         check_annotation_report(assembly_reports[ANNOTATION][assembly_id], assembly_id)
         assert assembly_reports[DATASET][assembly_id] is None
 
-    assert assembly_reports[ERROR] == [
-        {
-            "assembly_id": None,
-            "assembly_id_list": ALL_IDS,
-            "error_class": "HTTPError",
-            "error_from": "dataset_report",
-            "message": '404 Client Error: Not Found for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000\nResponse: {"error":"Not Found","code":404,"message":"Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
-            "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000",
-            "status": 404,
-            "reason": "Not Found",
-        }
-    ]
+    assert assembly_reports[ERROR] == [RECORDED_ERRORS["dataset_404"]]
 
 
 @mock.patch("tenacity.nap.time.sleep", MagicMock())
 @pytest.mark.vcr
 def test_get_assembly_reports_total_wipeout() -> None:
     """Test the retrieval of assembly data when all queries fail."""
-    # TODO: another type of error?
-    output = get_assembly_reports(ALL_IDS)
+    original_get_annotation_report = get_annotation_report
+
+    def patched_get_annotation_report(assembly_id: str) -> list[dict[str, Any]] | None:
+        """Patched version of get_annotation_report that throws a value error with a certain input.
+
+        :param assembly_id: assembly ID
+        :type assembly_id: str
+        :raises ValueError: if the ID is INVALID_ID
+        :return: output from the real get_annotation_report
+        :rtype: list[dict[str, Any]] | None
+        """
+        if assembly_id == INVALID_ID:
+            err_msg = f"Some error message involving {INVALID_ID}."
+            raise ValueError(err_msg)
+        return original_get_annotation_report(assembly_id)
+
+    with mock.patch(
+        "cdm_data_loaders.pipelines.ncbi_rest_api.get_annotation_report",
+        side_effect=patched_get_annotation_report,
+    ):
+        output = get_assembly_reports(ALL_IDS)
+
     assert output == {
         DATASET: dict.fromkeys(ALL_IDS),
         ANNOTATION: dict.fromkeys(ALL_IDS),
         ERROR: [
-            {
-                "assembly_id": None,
-                "assembly_id_list": ALL_IDS,
-                "error_class": "HTTPError",
-                "error_from": "dataset_report",
-                "message": '404 Client Error: Not Found for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000\nResponse: {"error":"Not Found","code":404,"message":"Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
-                "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1%2CGCF_000003135.1%2Cinvalid_id/dataset_report?page_size=1000",
-                "status": 404,
-                "reason": "Not Found",
-            },
-            {
-                "assembly_id": ID_WITH_500_ANNOTS,
-                "assembly_id_list": None,
-                "error_class": "HTTPError",
-                "error_from": "annotation_report",
-                "message": '404 Client Error: Not Found for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1/annotation_report?page_size=1000\nResponse: {"error":"Not Found","code":404,"message":"Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"}\n',
-                "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000007725.1/annotation_report?page_size=1000",
-                "status": 404,
-                "reason": "Not Found",
-            },
-            {
-                "assembly_id": ID_WITH_2K_ANNOTS,
-                "assembly_id_list": None,
-                "error_class": "HTTPError",
-                "error_from": "annotation_report",
-                "message": '500 Server Error: Internal Server Error for url: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw\nResponse: {"error":"Internal Server Error","code":500,"message":"Internal Server Error (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/) (1D32DF2AAA9FBB1500003B3C46C243D3.1.1)"}\n',
-                "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000003135.1/annotation_report?page_size=1000&page_token=eNrjYos2NDAwjAUABagBiw",
-                "status": 500,
-                "reason": "Internal Server Error",
-            },
+            RECORDED_ERRORS["dataset_404"],
+            RECORDED_ERRORS["annotation_report_404"],
+            RECORDED_ERRORS["annotation_report_500"],
+            RECORDED_ERRORS["value_error"],
         ],
     }
 
@@ -519,6 +506,169 @@ def test_get_assembly_reports_total_wipeout() -> None:
 @pytest.mark.skip("FIXME: not working, possibly due to parallelization?")
 @pytest.mark.vcr
 def test_get_assembly_report_parser_with_cassette(assembly_ids: list[str], tmp_path: Path) -> None:
-    with patch("dlt.mark") as mock_dlt_mark:
-        config = Settings.model_validate({"input_dir": "tests/data/ncbi_rest_api/input", "output": str(tmp_path)})
-        run_ncbi_pipeline(config)
+    with patch("dlt.mark"):
+        settings: NcbiSettings = make_settings_autofill_config(
+            NcbiSettings, input_dir="tests/data/ncbi_rest_api/input", output=str(tmp_path)
+        )  # type: ignore[reportAssignmentType]
+        run_ncbi_pipeline(settings)
+
+
+def collect_results(reports: dict) -> dict[str, list]:
+    """Drain the generator returned by assemble_assembly_reports into a dict keyed by table name."""
+    results: dict[str, list] = {}
+    for item in assemble_assembly_reports(reports):
+        assert isinstance(item, DataItemWithMeta), f"Expected DataItemWithMeta, got {type(item)}"
+        table_name = item.meta.table_name
+        results.setdefault(table_name, [])
+        results[table_name].extend(item.data)
+    return results
+
+
+# assemble_assembly_reports tests
+
+DATASET_REPORT_1 = {
+    "accession": ID_WITH_2K_ANNOTS,
+    "organism": {"tax_id": 9606, "organism_name": "Homo sapiens"},
+    "assembly_stats": {"total_sequence_length": 3099734149},
+}
+
+DATASET_REPORT_2 = {
+    "accession": ID_WITH_500_ANNOTS,
+    "organism": {"tax_id": 10090, "organism_name": "Mus musculus"},
+    "assembly_stats": {"total_sequence_length": 2728222451},
+}
+
+ANNOTATION_REPORT_1 = [
+    {"release_date": "2022-01-01", "annotation_name": "Annotation A"},
+    {"release_date": "2022-06-01", "annotation_name": "Annotation B"},
+]
+
+ANNOTATION_REPORT_2 = [
+    {"release_date": "2023-01-01", "annotation_name": "Annotation C"},
+]
+
+ERROR_REPORT = {
+    "assembly_id": INVALID_ID,
+    "assembly_id_list": None,
+    "error_class": "HTTPError",
+    "error_from": "dataset_report",
+    "message": "404 Not Found",
+    "request_url": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCA_000001635.9/dataset_report",
+    "status": 404,
+    "reason": "Not Found",
+}
+
+
+@pytest.fixture
+def full_assembly_reports() -> dict[str, Any]:
+    """Assembly reports fixture with valid data for two assemblies and no errors."""
+    return {
+        DATASET: {
+            ID_WITH_2K_ANNOTS: DATASET_REPORT_1,
+            ID_WITH_500_ANNOTS: DATASET_REPORT_2,
+        },
+        ANNOTATION: {
+            ID_WITH_2K_ANNOTS: ANNOTATION_REPORT_1,
+            ID_WITH_500_ANNOTS: ANNOTATION_REPORT_2,
+        },
+        ERROR: [],
+    }
+
+
+@pytest.fixture
+def reports_with_errors() -> dict[str, Any]:
+    """Assembly reports fixture with one None dataset report, one None annotation report, and one error entry."""
+    return {
+        DATASET: {
+            ID_WITH_2K_ANNOTS: DATASET_REPORT_1,
+            ID_WITH_500_ANNOTS: DATASET_REPORT_2,
+            INVALID_ID: None,
+        },
+        ANNOTATION: {
+            ID_WITH_2K_ANNOTS: ANNOTATION_REPORT_1,
+            ID_WITH_500_ANNOTS: ANNOTATION_REPORT_2,
+            INVALID_ID: None,
+        },
+        ERROR: [ERROR_REPORT],
+    }
+
+
+EXPECTED_DB_TABLES = {
+    f"{DATASET}_report": [
+        {"assembly_id": ID_WITH_2K_ANNOTS, **DATASET_REPORT_1},
+        {
+            "assembly_id": ID_WITH_500_ANNOTS,
+            **DATASET_REPORT_2,
+        },
+    ],
+    f"{ANNOTATION}_report": [
+        {"assembly_id": ID_WITH_2K_ANNOTS, **ANNOTATION_REPORT_1[0]},
+        {"assembly_id": ID_WITH_2K_ANNOTS, **ANNOTATION_REPORT_1[1]},
+        {"assembly_id": ID_WITH_500_ANNOTS, **ANNOTATION_REPORT_2[0]},
+    ],
+}
+
+EXPECTED_DB_TABLES_WITH_ERROR = {
+    f"{DATASET}_report": [*EXPECTED_DB_TABLES[f"{DATASET}_report"], {"assembly_id": INVALID_ID}],
+    f"{ANNOTATION}_report": [*EXPECTED_DB_TABLES[f"{ANNOTATION}_report"]],
+    "ncbi_import_error": [ERROR_REPORT],
+}
+
+
+@pytest.mark.parametrize("reports", [{}, None])
+def test_assemble_assembly_reports_empty_dict_yields_nothing(reports: None | dict[str, Any]) -> None:
+    """Ensure that empty or None as input produces no output items."""
+    assert list(assemble_assembly_reports(reports)) == []  # type: ignore[reportArgumentType]
+
+
+def test_assemble_assembly_reports_yields_two_items_when_no_errors(full_assembly_reports: dict[str, Any]) -> None:
+    """When the error list is empty, the generator should yield only two DataItemWithMeta objects."""
+    assert len(list(assemble_assembly_reports(full_assembly_reports))) == 2
+
+
+def test_assemble_assembly_reports_all_items_are_data_item_with_meta(full_assembly_reports: dict[str, Any]) -> None:
+    """Every item yielded by the generator should be a DataItemWithMeta instance."""
+    for item in assemble_assembly_reports(full_assembly_reports):
+        assert isinstance(item, DataItemWithMeta)
+
+
+def test_assemble_assembly_reports_table_names_when_errors_present(reports_with_errors: dict[str, Any]) -> None:
+    """The output should contain dataset_report, annotation_report, and ncbi_import_error table names."""
+    results = collect_results(reports_with_errors)
+    assert set(results) == {"dataset_report", "annotation_report", "ncbi_import_error"}
+    assert results == EXPECTED_DB_TABLES_WITH_ERROR
+
+
+def test_assemble_assembly_reports_no_error_table_when_error_list_empty(full_assembly_reports: dict[str, Any]) -> None:
+    """When the error list is empty, no ncbi_import_error table should be present in the output."""
+    results = collect_results(full_assembly_reports)
+    assert set(results) == {"dataset_report", "annotation_report"}
+    assert results == EXPECTED_DB_TABLES
+
+
+def test_assemble_assembly_reports_dataset_report_none_report_emits_row_with_only_assembly_id() -> None:
+    """A None dataset report should still produce a row containing only the assembly_id key."""
+    reports = {
+        DATASET: {INVALID_ID: None},
+        ANNOTATION: {INVALID_ID: None},
+        ERROR: [],
+    }
+    results = collect_results(reports)
+    # no ncbi_import_error or annotation_report
+    assert results["dataset_report"] == [{"assembly_id": INVALID_ID}]
+
+
+def test_assemble_assembly_reports_multiple_errors_all_yielded() -> None:
+    """All entries in the error list should appear as individual rows in the ncbi_import_error table."""
+    errors = [
+        {"error_class": "HTTPError", "error_from": "dataset_report", "message": "err1"},
+        {"error_class": "ValueError", "error_from": "annotation_report", "message": "err2"},
+    ]
+    reports = {
+        DATASET: {},
+        ANNOTATION: {},
+        ERROR: errors,
+    }
+    results = collect_results(reports)
+    assert results["ncbi_import_error"] == errors
+    assert set(results) == {"ncbi_import_error"}
diff --git a/tests/pipelines/test_uniprot.py b/tests/pipelines/test_uniprot.py
index af746fac..56e3028b 100644
--- a/tests/pipelines/test_uniprot.py
+++ b/tests/pipelines/test_uniprot.py
@@ -1,4 +1,4 @@
-"""Tests for the UniProtDLT pipeline."""
+"""Tests for the UniProt DLT pipeline."""
 
 import datetime
 from collections.abc import Callable
@@ -7,163 +7,158 @@
 from unittest.mock import MagicMock, patch
 
 import pytest
-from pydantic import ValidationError
+from frozendict import frozendict
 from pydantic_settings import CliApp
 
 from cdm_data_loaders.parsers.uniprot.uniprot_kb import ENTRY_XML_TAG
+from cdm_data_loaders.pipelines import core
 from cdm_data_loaders.pipelines import uniprot_kb as uniprot_module
-from cdm_data_loaders.pipelines.cts_defaults import INPUT_MOUNT, VALID_DESTINATIONS
+from cdm_data_loaders.pipelines.cts_defaults import ARG_ALIASES
 from cdm_data_loaders.pipelines.uniprot_kb import (
     UNIPROT_LOG_INTERVAL,
-    Settings,
+    UniProtSettings,
     cli,
     parse_uniprot,
     run_uniprot_pipeline,
 )
-from tests.pipelines.conftest import make_batcher
+from tests.pipelines.conftest import (
+    TEST_BATCH_FILE_SETTINGS,
+    TEST_BATCH_FILE_SETTINGS_RECONCILED,
+    check_settings,
+    make_batcher,
+    make_settings_autofill_config,
+)
 
 # TODO: add a test to ensure that parse_uniprot_entry is called with the appropriate args. Requires mocking the file batcher and stream_xml_file_resource functions.
 
 
-@pytest.fixture
-def config() -> Settings:
-    """Provide a minimal valid Settings object."""
-    return make_settings(input_dir="/fake/input")
-
-
-START_AT_VALUE = 50
-START_AT_STRING = "50"
+@pytest.fixture(autouse=True)
+def patch_dlt_config(dlt_config: dict[str, Any], monkeypatch: pytest.MonkeyPatch) -> None:
+    """Monkeypatch the dlt config in all tests."""
+    monkeypatch.setattr(core.dlt, "config", dlt_config)
 
 
-def make_settings(**kwargs: str | int) -> Settings:
-    """Generate a validated Settings object."""
-    return Settings.model_validate(kwargs)
-
+@pytest.fixture
+def test_settings() -> UniProtSettings:
+    """Provide a minimal valid UniProtSettings object."""
+    return make_settings_autofill_config(UniProtSettings)  # type: ignore[reportReturnType]
 
-def test_settings_defaults() -> None:
-    """Ensure the settings defaults are set up correctly."""
-    s = make_settings()
-    assert s.destination == "local_fs"
-    assert s.start_at == 0
-    assert s.output is None
-    assert s.input_dir == INPUT_MOUNT
 
+TEST_SETTINGS = frozendict(
+    **TEST_BATCH_FILE_SETTINGS,
+)
 
-def test_settings_all_params_set() -> None:
-    """Ensure that settings are set correctly when all args are specified."""
-    s = make_settings(
-        input_dir="/dir/path",
-        destination=VALID_DESTINATIONS[0],
-        start_at=START_AT_STRING,
-        output="/some/dir",
-    )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
+TEST_SETTINGS_RECONCILED = frozendict(
+    **TEST_BATCH_FILE_SETTINGS_RECONCILED,
+)
 
 
-@pytest.mark.parametrize("destination", VALID_DESTINATIONS)
-def test_settings_valid_variants_accepted(destination: str) -> None:
-    """Ensure that each valid destination value is accepted without error."""
-    s = make_settings(destination=destination)
-    assert s.destination == destination
+def test_make_settings_all_params_set() -> None:
+    """Ensure that settings are set correctly when all args are specified.
 
+    Note that TEST_SETTINGS includes a value for pipeline_dir.
+    """
+    s = make_settings_autofill_config(UniProtSettings, **TEST_SETTINGS)  # type: ignore[reportReturnType]
+    check_settings(s, TEST_SETTINGS_RECONCILED)
 
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_invalid_destination_raises(bad: str) -> None:
-    """Ensure that an unrecognised destination raises a ValidationError."""
-    with pytest.raises(ValidationError, match="destination must be one of"):
-        make_settings(destination=bad)
 
+@pytest.mark.parametrize("dev_mode", ARG_ALIASES["dev_mode"])
+@pytest.mark.parametrize("input_dir", ARG_ALIASES["input_dir"])
+@pytest.mark.parametrize("output", ARG_ALIASES["output"])
+@pytest.mark.parametrize("start_at", ARG_ALIASES["start_at"])
+@pytest.mark.parametrize("use_destination", ARG_ALIASES["use_destination"])
+@pytest.mark.parametrize(
+    "use_output_dir_for_pipeline_metadata",
+    ARG_ALIASES["use_output_dir_for_pipeline_metadata"],
+)
+def test_cli_app_run_alt_settings(  # noqa: PLR0913
+    dev_mode: str,
+    input_dir: str,
+    output: str,
+    start_at: str,
+    use_destination: str,
+    use_output_dir_for_pipeline_metadata: str,
+    dlt_config: dict[str, Any],
+) -> None:
+    """Test all the variants of the UniProtSettings fields."""
+    cli_args = [
+        dev_mode,
+        TEST_SETTINGS["dev_mode"],
+        input_dir,
+        TEST_SETTINGS["input_dir"],
+        output,
+        TEST_SETTINGS["output"],
+        start_at,
+        TEST_SETTINGS["start_at"],
+        use_destination,
+        TEST_SETTINGS["use_destination"],
+        use_output_dir_for_pipeline_metadata,
+        TEST_SETTINGS["use_output_dir_for_pipeline_metadata"],
+    ]
 
-@pytest.mark.parametrize("input_dir", ["-i", "--input-dir", "--input_dir"])
-@pytest.mark.parametrize("destination", ["-d", "--destination"])
-@pytest.mark.parametrize("start_at", ["-s", "--start-at", "--start_at"])
-@pytest.mark.parametrize("output", ["-o", "--output"])
-def test_cli_all_variants(input_dir: str, destination: str, start_at: str, output: str) -> None:
-    """Test all the variants of the Settings fields."""
     s = CliApp.run(
-        Settings,
-        [
-            input_dir,
-            "/dir/path",
-            destination,
-            VALID_DESTINATIONS[0],
-            start_at,
-            START_AT_STRING,
-            output,
-            "/some/dir",
-        ],
+        UniProtSettings,
+        dlt_config=dlt_config,
+        cli_args=cli_args,
     )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
-
-
-@pytest.mark.parametrize("bad", ["gcs", "filesystem", "", "LocalFs"])
-def test_cli_invalid_destination_via_cli_raises(bad: str) -> None:
-    """Ensure that an invalid destination passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match="Value error, destination must be one of"):
-        CliApp.run(Settings, cli_args=["--destination", bad])
+    check_settings(s, TEST_SETTINGS_RECONCILED)
 
 
 def test_cli_passes_settings_class_to_run_cli() -> None:
-    """Ensure that cli() calls run_cli with Settings as the settings class."""
+    """Ensure that cli() calls run_cli with UniProtSettings as the settings class."""
     with patch.object(uniprot_module, "run_cli") as mock_run_cli:
         cli()
 
     mock_run_cli.assert_called_once()
-    assert mock_run_cli.call_args[0] == (Settings, run_uniprot_pipeline)
+    assert mock_run_cli.call_args[0] == (UniProtSettings, run_uniprot_pipeline)
 
 
-def test_cli_calls_run_uniprot_pipeline(monkeypatch: pytest.MonkeyPatch) -> None:
-    """Ensure that cli() calls run_uniprot_pipeline with the config."""
-    mock_settings_instance = MagicMock(spec=Settings)
+def test_cli_calls_run_uniprot_pipeline(monkeypatch: pytest.MonkeyPatch, dlt_config: dict[str, Any]) -> None:
+    """Ensure that cli() calls run_uniprot_pipeline with the test_settings."""
+    mock_settings_instance = MagicMock()
     mock_settings_cls = MagicMock(return_value=mock_settings_instance)
     mock_run_uniprot_pipeline = MagicMock()
 
-    monkeypatch.setattr(uniprot_module, "Settings", mock_settings_cls)
+    monkeypatch.setattr(uniprot_module, "UniProtSettings", mock_settings_cls)
     monkeypatch.setattr(uniprot_module, "run_uniprot_pipeline", mock_run_uniprot_pipeline)
 
     cli()
 
-    mock_settings_cls.assert_called_once_with()
+    mock_settings_cls.assert_called_once_with(dlt_config=dlt_config)
     mock_run_uniprot_pipeline.assert_called_once_with(mock_settings_instance)
 
 
 # Tests for running the pipeline itself
-def test_run_uniprot_pipeline_args_set_correctly(config: Settings) -> None:
+def test_run_uniprot_pipeline_args_set_correctly(test_settings: UniProtSettings) -> None:
     """Ensure that the pipeline arguments are set correctly, and each pipeline has a different name."""
     with patch.object(uniprot_module, "run_pipeline") as mock_run_pipeline:
-        run_uniprot_pipeline(config)
+        run_uniprot_pipeline(test_settings)
 
     assert mock_run_pipeline.call_count == 1
     _, kwargs = mock_run_pipeline.call_args
-    assert kwargs.keys() == {"config", "resource", "pipeline_kwargs", "pipeline_run_kwargs"}
+    assert kwargs.keys() == {"settings", "resource", "pipeline_kwargs", "pipeline_run_kwargs"}
     assert kwargs["pipeline_kwargs"] == {"pipeline_name": "uniprot_kb", "dataset_name": "uniprot_kb"}
     assert kwargs["pipeline_run_kwargs"] == {"table_format": "delta"}
-    assert kwargs["config"] == config
+    assert kwargs["settings"] == test_settings
     assert isinstance(kwargs["resource"], Callable)
 
 
 def test_run_uniprot_pipeline_sets_core_run_pipeline_args_correctly(
-    config: Settings, mock_dlt: MagicMock, monkeypatch: pytest.MonkeyPatch
+    test_settings: UniProtSettings, mock_dlt: MagicMock, monkeypatch: pytest.MonkeyPatch
 ) -> None:
     """Ensure that run_uniprot_pipeline calls core.run_pipeline with the correct args."""
     mock_parse_uniprot = MagicMock()
     monkeypatch.setattr(uniprot_module, "parse_uniprot", mock_parse_uniprot)
 
-    run_uniprot_pipeline(config)
+    run_uniprot_pipeline(test_settings)
 
-    # parse_uniprot was called once with the config to produce the resource
-    mock_parse_uniprot.assert_called_once_with(config)
+    # parse_uniprot was called once with the test_settings to produce the resource
+    mock_parse_uniprot.assert_called_once_with(test_settings)
 
-    # the return value of parse_uniprot(config) is what gets passed to pipeline.run
+    # the return value of parse_uniprot(test_settings) is what gets passed to pipeline.run
     expected_resource = mock_parse_uniprot.return_value
 
-    mock_dlt.destination.assert_called_once_with(config.destination)
+    mock_dlt.destination.assert_called_once_with(test_settings.use_destination)
     mock_dlt.pipeline.assert_called_once_with(
         destination=mock_dlt.destination.return_value,
         pipeline_name="uniprot_kb",
@@ -175,24 +170,24 @@ def test_run_uniprot_pipeline_sets_core_run_pipeline_args_correctly(
     )
 
 
-def test_parse_uniprot_resource(config: Settings) -> None:
+def test_parse_uniprot_resource(test_settings: UniProtSettings) -> None:
     """Ensure that parse_uniprot calls stream_xml_file_resource with the namespaced UniProt XML tag."""
     with patch.object(uniprot_module, "stream_xml_file_resource") as mock_stream:
         mock_stream.return_value = iter([])
-        list(parse_uniprot(config))
+        list(parse_uniprot(test_settings))
 
     assert mock_stream.call_count == 1
     kwargs = mock_stream.call_args.kwargs
-    assert kwargs.keys() == {"config", "xml_tag", "parse_fn", "log_interval"}
+    assert kwargs.keys() == {"settings", "xml_tag", "parse_fn", "log_interval"}
     assert kwargs["xml_tag"] == ENTRY_XML_TAG
     assert kwargs["log_interval"] == UNIPROT_LOG_INTERVAL
-    assert kwargs["config"] == config
+    assert kwargs["settings"] == test_settings
     assert isinstance(kwargs["parse_fn"], Callable)
 
 
 @pytest.mark.skip("FIXME: not working -- due to parallelization?")
 def test_integration_cli_uniprot_pipeline_output_validated(
-    config: Settings,  # the uniprot_kb Settings fixture
+    test_settings: UniProtSettings,  # the uniprot_kb UniProtSettings fixture
     fake_files: list[Path],
     mock_dlt: MagicMock,
     patched_io: tuple[MagicMock, MagicMock],
@@ -223,16 +218,17 @@ def fake_parse_uniprot_entry(
     # make pipeline.run actually drain the generator so all assertions fire
     mock_dlt.pipeline.return_value.run.side_effect = lambda resource, **_: list(resource)
 
-    # exercise the real cli() wiring with Settings construction mocked out
-    monkeypatch.setattr(uniprot_module, "Settings", MagicMock(return_value=config))
+    # exercise the real cli() wiring with UniProtSettings construction mocked out
+    monkeypatch.setattr(uniprot_module, "UniProtSettings", MagicMock(return_value=test_settings))
     cli()
 
     mock_dlt.pipeline.assert_called_once_with(
         pipeline_name="uniprot_kb",
         destination=mock_dlt.destination.return_value,
         dataset_name="uniprot_kb",
+        dev_mode=False,
     )
-    mock_dlt.destination.assert_called_once_with(config.destination)
+    mock_dlt.destination.assert_called_once_with(test_settings.use_destination)
     mock_dlt.pipeline.return_value.run.assert_called_once()
 
     # verify with_table_name received the right rows and table names for every file, in order
diff --git a/tests/pipelines/test_uniref.py b/tests/pipelines/test_uniref.py
index da5899ec..fe9deb68 100644
--- a/tests/pipelines/test_uniref.py
+++ b/tests/pipelines/test_uniref.py
@@ -1,4 +1,4 @@
-"""Tests for the uniref DLT pipeline."""
+"""Tests for the UniRef DLT pipeline."""
 
 import datetime
 from collections.abc import Callable
@@ -7,14 +7,29 @@
 from unittest.mock import MagicMock, patch
 
 import pytest
+from frozendict import frozendict
 from pydantic import ValidationError
 from pydantic_settings import CliApp
 
 from cdm_data_loaders.parsers.uniprot.uniref import ENTRY_XML_TAG, UNIREF_VARIANTS
+from cdm_data_loaders.pipelines import core
 from cdm_data_loaders.pipelines import uniref as uniref_module
-from cdm_data_loaders.pipelines.cts_defaults import INPUT_MOUNT, VALID_DESTINATIONS
-from cdm_data_loaders.pipelines.uniref import UNIREF_LOG_INTERVAL, Settings, cli, parse_uniref, run_uniref_pipeline
-from tests.pipelines.conftest import make_batcher
+from cdm_data_loaders.pipelines.cts_defaults import ARG_ALIASES
+from cdm_data_loaders.pipelines.uniref import (
+    UNIREF_LOG_INTERVAL,
+    UNIREF_VARIANT_ALIASES,
+    UnirefSettings,
+    cli,
+    parse_uniref,
+    run_uniref_pipeline,
+)
+from tests.pipelines.conftest import (
+    TEST_BATCH_FILE_SETTINGS,
+    TEST_BATCH_FILE_SETTINGS_RECONCILED,
+    check_settings,
+    make_batcher,
+    make_settings_autofill_config,
+)
 
 # TODO: add a test to ensure that parse_uniref_entry is called with the appropriate args. Requires mocking the file batcher and stream_xml_file_resource functions.
 
@@ -25,10 +40,21 @@
 TEST_DEFAULT_UNIREF_VARIANT = "50"
 
 
-def make_settings(uniref_variant: str = TEST_DEFAULT_UNIREF_VARIANT, **kwargs: str | int) -> Settings:
-    """Generate a validated Settings object."""
-    data = {"uniref": uniref_variant, **kwargs}
-    return Settings.model_validate(data)
+TEST_SETTINGS = frozendict(
+    **TEST_BATCH_FILE_SETTINGS,
+    uniref_variant=TEST_DEFAULT_UNIREF_VARIANT,
+)
+
+TEST_SETTINGS_RECONCILED = frozendict(
+    **TEST_BATCH_FILE_SETTINGS_RECONCILED,
+    uniref_variant=TEST_DEFAULT_UNIREF_VARIANT,
+)
+
+
+@pytest.fixture(autouse=True)
+def patch_dlt_config(dlt_config: dict[str, Any], monkeypatch: pytest.MonkeyPatch) -> None:
+    """Monkeypatch the dlt config in all tests."""
+    monkeypatch.setattr(core.dlt, "config", dlt_config)
 
 
 @pytest.fixture(params=UNIREF_VARIANTS)
@@ -38,183 +64,204 @@ def variant(request: pytest.FixtureRequest) -> str:
 
 
 @pytest.fixture
-def config(variant: str) -> Settings:
-    """A valid Settings object for each uniref variant."""
-    return make_settings(uniref_variant=variant, input_dir="/fake/input")
-
-
-def test_settings_defaults() -> None:
-    """Ensure the settings defaults are set up correctly."""
-    s = make_settings()
-    assert s.destination == "local_fs"
-    assert s.start_at == 0
-    assert s.output is None
-    assert s.input_dir == INPUT_MOUNT
-    assert s.uniref_variant == TEST_DEFAULT_UNIREF_VARIANT
-
-
-def test_settings_all_params_set() -> None:
-    """Ensure that settings are set correctly when all args are specified."""
-    s = make_settings(
-        input_dir="/dir/path",
-        destination=VALID_DESTINATIONS[0],
-        uniref_variant="100",
-        start_at=START_AT_STRING,
-        output="/some/dir",
-    )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.uniref_variant == "100"
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
+def test_settings(variant: str) -> UnirefSettings:
+    """A valid UnirefSettings object for each uniref variant."""
+    return make_settings_autofill_config(UnirefSettings, uniref_variant=variant, input_dir="/fake/input")  # type: ignore[reportReturnType]
 
 
-@pytest.mark.parametrize("destination", VALID_DESTINATIONS)
-@pytest.mark.parametrize("uniref_variant", UNIREF_VARIANTS)
-def test_settings_valid_variants_accepted(uniref_variant: str, destination: str) -> None:
+@pytest.mark.parametrize("variant", UNIREF_VARIANTS)
+def test_settings_valid_variants_accepted(variant: str) -> None:
     """Ensure that each valid uniref_variant value is accepted without error."""
-    s = make_settings(uniref_variant=uniref_variant, destination=destination)
-    assert s.uniref_variant == uniref_variant
-    assert s.destination == destination
+    s = make_settings_autofill_config(UnirefSettings, uniref_variant=variant)
+    assert isinstance(s, UnirefSettings)
+    assert s.uniref_variant == variant
 
 
-@pytest.mark.parametrize("bad_variant", ["25", "75", "uniref50", "", "ALL"])
-def test_invalid_variant_raises(bad_variant: str) -> None:
-    """Ensure that an unrecognised uniref_variant raises a ValidationError."""
-    with pytest.raises(ValidationError, match="uniref_variant must be one of"):
-        make_settings(uniref_variant=bad_variant)
-
+@pytest.mark.parametrize("value", UNIREF_VARIANTS)
+@pytest.mark.parametrize("uniref_variant", UNIREF_VARIANT_ALIASES)
+def test_cli_valid_variants_accepted(uniref_variant: str, dlt_config: dict[str, Any], value: str) -> None:
+    """Ensure that each valid uniref_variant value is accepted without error when passed via CLI."""
+    s = CliApp.run(UnirefSettings, dlt_config=dlt_config, cli_args=[uniref_variant, value])
+    assert isinstance(s, UnirefSettings)
+    assert s.uniref_variant == value
 
-@pytest.mark.parametrize("bad_destination", ["gcs", "filesystem", "", "LocalFs"])
-def test_invalid_destination_raises(bad_destination: str) -> None:
-    """Ensure that an unrecognised destination raises a ValidationError."""
-    with pytest.raises(ValidationError, match="destination must be one of"):
-        make_settings(destination=bad_destination)
 
+@pytest.mark.parametrize("value", ["25", "75", "uniref50", "", "ALL"])
+def test_invalid_variant_raises(value: str) -> None:
+    """Ensure that an unrecognised uniref_variant raises a ValidationError."""
+    with pytest.raises(ValidationError, match="1 validation error for UnirefSettings") as exc_info:
+        make_settings_autofill_config(UnirefSettings, uniref_variant=value)
 
-@pytest.mark.parametrize("input_dir", ["-i", "--input-dir", "--input_dir"])
-@pytest.mark.parametrize("destination", ["-d", "--destination"])
-@pytest.mark.parametrize("uniref_variant", ["-u", "--uniref", "--uniref-variant", "--uniref_variant"])
-@pytest.mark.parametrize("start_at", ["-s", "--start-at", "--start_at"])
-@pytest.mark.parametrize("output", ["-o", "--output"])
-def test_cli_all_variants(input_dir: str, destination: str, uniref_variant: str, start_at: str, output: str) -> None:
-    """Test all the variants of the Settings fields."""
-    s = CliApp.run(
-        Settings,
-        [
-            input_dir,
-            "/dir/path",
-            destination,
-            VALID_DESTINATIONS[0],
-            uniref_variant,
-            TEST_DEFAULT_UNIREF_VARIANT,
-            start_at,
-            START_AT_STRING,
-            output,
-            "/some/dir",
-        ],
-    )
-    assert s.input_dir == "/dir/path"
-    assert s.destination == VALID_DESTINATIONS[0]
-    assert s.uniref_variant == TEST_DEFAULT_UNIREF_VARIANT
-    assert s.start_at == START_AT_VALUE
-    assert s.output == "/some/dir"
+    exc_message = str(exc_info.value)
+    assert "uniref_variant must be one of" in exc_message
 
 
-@pytest.mark.parametrize("bad_variant", ["25", "75", "uniref50", "", "ALL"])
-def test_cli_invalid_variant_via_cli_raises(bad_variant: str) -> None:
+@pytest.mark.parametrize("value", ["25", "75", "uniref50", "", "ALL"])
+@pytest.mark.parametrize("uniref_variant", UNIREF_VARIANT_ALIASES)
+def test_cli_invalid_variant_via_cli_raises(value: str, uniref_variant: str, dlt_config: dict[str, Any]) -> None:
     """Ensure that an invalid uniref_variant passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match="Value error, uniref_variant must be one of"):
-        CliApp.run(Settings, cli_args=["--uniref-variant", bad_variant])
+    # with pytest.raises(ValidationError, match="Value error, uniref_variant must be one of"):
+    with pytest.raises(ValidationError, match="1 validation error for UnirefSettings") as exc_info:
+        CliApp.run(UnirefSettings, dlt_config=dlt_config, cli_args=[uniref_variant, value])
+
+    exc_message = str(exc_info.value)
+    assert "Value error, uniref_variant must be one of" in exc_message
 
 
-@pytest.mark.parametrize("bad_destination", ["25", "75", "uniref50", "", "ALL"])
-def test_cli_invalid_destination_via_cli_raises(bad_destination: str) -> None:
-    """Ensure that an invalid destination passed via CLI raises an error."""
-    with pytest.raises(ValidationError, match="Value error, destination must be one of"):
-        CliApp.run(Settings, cli_args=["--uniref-variant", "50", "--destination", bad_destination])
+def test_missing_required_uniref_variant_raises() -> None:
+    """Ensure that omitting the required uniref_variant argument raises a ValidationError."""
+    with pytest.raises(ValidationError, match="1 validation error for UnirefSettings") as exc_info:
+        make_settings_autofill_config(UnirefSettings)
+
+    exc_message = str(exc_info.value)
+    assert "Field required" in exc_message
 
 
-def test_cli_missing_required_uniref_variant_raises() -> None:
+def test_cli_missing_required_uniref_variant_raises(dlt_config: dict[str, Any]) -> None:
     """Ensure that omitting the required uniref_variant argument raises an error."""
-    with pytest.raises(ValidationError, match="Field required"):
-        CliApp.run(Settings, cli_args=[])
+    with pytest.raises(ValidationError, match="1 validation error for UnirefSettings") as exc_info:
+        CliApp.run(UnirefSettings, dlt_config=dlt_config, cli_args=[])
 
+    exc_message = str(exc_info.value)
+    assert "Field required" in exc_message
 
-@pytest.mark.parametrize("bad_variant", ["25", "75", "uniref50", "", "ALL"])
-@pytest.mark.parametrize("bad_destination", ["gcs", "filesystem", "", "LocalFs"])
-def test_cli_invalid_variant_and_destination_via_cli_raises(bad_variant: str, bad_destination: str) -> None:
-    """Ensure that invalid uniref_variant and destination passed via CLI raises an error with both errors."""
-    with pytest.raises(ValidationError, match="2 validation errors for Settings") as exc_info:
-        CliApp.run(Settings, cli_args=["--uniref-variant", bad_variant, "--destination", bad_destination])
+
+@pytest.mark.parametrize("value", ["25", "75", "uniref50", "", "ALL"])
+@pytest.mark.parametrize("uniref_variant", UNIREF_VARIANT_ALIASES)
+def test_cli_invalid_variant_and_destination_via_cli_raises(
+    value: str, uniref_variant: str, dlt_config: dict[str, Any]
+) -> None:
+    """Ensure that invalid uniref_variant and use_destination passed via CLI raises an error with both errors.
+
+    N.b. Pydantic only reports the first error!!!
+    """
+    with pytest.raises(ValidationError, match="1 validation error for UnirefSettings") as exc_info:
+        CliApp.run(
+            UnirefSettings,
+            dlt_config=dlt_config,
+            cli_args=[uniref_variant, value, "--use_destination", "some invalid destination"],
+        )
 
     # Check that both errors are present in the exception message
     exc_message = str(exc_info.value)
     assert "Value error, uniref_variant must be one of" in exc_message
-    assert "Value error, destination must be one of" in exc_message
+
+
+def test_make_settings_all_params_set() -> None:
+    """Ensure that settings are set correctly when all args are specified.
+
+    Note that TEST_SETTINGS includes a value for pipeline_dir.
+    """
+    s = make_settings_autofill_config(UnirefSettings, **TEST_SETTINGS)
+    check_settings(s, TEST_SETTINGS_RECONCILED)
+
+
+@pytest.mark.parametrize("dev_mode", ARG_ALIASES["dev_mode"])
+@pytest.mark.parametrize("input_dir", ARG_ALIASES["input_dir"])
+@pytest.mark.parametrize("output", ARG_ALIASES["output"])
+@pytest.mark.parametrize("start_at", ARG_ALIASES["start_at"])
+@pytest.mark.parametrize("uniref_variant", UNIREF_VARIANT_ALIASES)
+@pytest.mark.parametrize("use_destination", ARG_ALIASES["use_destination"])
+@pytest.mark.parametrize(
+    "use_output_dir_for_pipeline_metadata",
+    ARG_ALIASES["use_output_dir_for_pipeline_metadata"],
+)
+def test_cli_app_run_alt_settings(  # noqa: PLR0913
+    dev_mode: str,
+    input_dir: str,
+    output: str,
+    start_at: str,
+    uniref_variant: str,
+    use_destination: str,
+    use_output_dir_for_pipeline_metadata: str,
+    dlt_config,
+) -> None:
+    """Test all the variants of the UnirefSettings fields."""
+    cli_args = [
+        dev_mode,
+        TEST_SETTINGS["dev_mode"],
+        input_dir,
+        TEST_SETTINGS["input_dir"],
+        output,
+        TEST_SETTINGS["output"],
+        start_at,
+        TEST_SETTINGS["start_at"],
+        uniref_variant,
+        TEST_SETTINGS["uniref_variant"],
+        use_destination,
+        TEST_SETTINGS["use_destination"],
+        use_output_dir_for_pipeline_metadata,
+        TEST_SETTINGS["use_output_dir_for_pipeline_metadata"],
+    ]
+
+    s = CliApp.run(
+        UnirefSettings,
+        dlt_config=dlt_config,
+        cli_args=cli_args,
+    )
+    check_settings(s, TEST_SETTINGS_RECONCILED)
 
 
 def test_cli_passes_settings_class_to_run_cli() -> None:
-    """Ensure that cli() calls run_cli with Settings as the settings class."""
+    """Ensure that cli() calls run_cli with UnirefSettings as the settings class."""
     with patch.object(uniref_module, "run_cli") as mock_run_cli:
         cli()
 
     mock_run_cli.assert_called_once()
-    assert mock_run_cli.call_args[0] == (Settings, run_uniref_pipeline)
+    assert mock_run_cli.call_args[0] == (UnirefSettings, run_uniref_pipeline)
 
 
-def test_cli_calls_run_uniref_pipeline(monkeypatch: pytest.MonkeyPatch) -> None:
-    """Ensure that cli() calls run_uniref_pipeline with the config."""
-    mock_settings_instance = MagicMock(spec=Settings)
+def test_cli_calls_run_uniref_pipeline(monkeypatch: pytest.MonkeyPatch, dlt_config: dict[str, Any]) -> None:
+    """Ensure that cli() calls run_uniref_pipeline with the settings."""
+    mock_settings_instance = MagicMock()
     mock_settings_cls = MagicMock(return_value=mock_settings_instance)
     mock_run_uniref_pipeline = MagicMock()
 
-    monkeypatch.setattr(uniref_module, "Settings", mock_settings_cls)
+    monkeypatch.setattr(uniref_module, "UnirefSettings", mock_settings_cls)
     monkeypatch.setattr(uniref_module, "run_uniref_pipeline", mock_run_uniref_pipeline)
 
     cli()
-    # no args
-    mock_settings_cls.assert_called_once_with()
+    mock_settings_cls.assert_called_once_with(dlt_config=dlt_config)
     mock_run_uniref_pipeline.assert_called_once_with(mock_settings_instance)
 
 
 # Tests for running the pipeline itself
-def test_run_uniref_pipeline_args_set_correctly(config: Settings) -> None:
+def test_run_uniref_pipeline_args_set_correctly(test_settings: UnirefSettings) -> None:
     """Ensure that the pipeline arguments are set correctly, and each pipeline has a different name."""
     with patch.object(uniref_module, "run_pipeline") as mock_run_pipeline:
-        run_uniref_pipeline(config)
+        run_uniref_pipeline(test_settings)
 
     assert mock_run_pipeline.call_count == 1
     _, kwargs = mock_run_pipeline.call_args
-    assert kwargs.keys() == {"config", "resource", "pipeline_kwargs", "pipeline_run_kwargs"}
+    assert kwargs.keys() == {"settings", "resource", "pipeline_kwargs", "pipeline_run_kwargs"}
     assert kwargs["pipeline_kwargs"] == {
-        "pipeline_name": f"uniref_{config.uniref_variant}",
+        "pipeline_name": f"uniref_{test_settings.uniref_variant}",
         "dataset_name": "uniprot_kb",
     }
     assert kwargs["pipeline_run_kwargs"] == {"table_format": "delta"}
-    assert kwargs["config"] == config
+    assert kwargs["settings"] == test_settings
     assert isinstance(kwargs["resource"], Callable)
 
 
 def test_run_uniref_pipeline_sets_core_run_pipeline_args_correctly(
-    config: Settings, mock_dlt: MagicMock, monkeypatch: pytest.MonkeyPatch
+    test_settings: UnirefSettings, mock_dlt: MagicMock, monkeypatch: pytest.MonkeyPatch
 ) -> None:
     """Ensure that run_uniref_pipeline calls core.run_pipeline with the correct args."""
     mock_parse_uniref = MagicMock()
     monkeypatch.setattr(uniref_module, "parse_uniref", mock_parse_uniref)
 
-    run_uniref_pipeline(config)
+    run_uniref_pipeline(test_settings)
 
-    # parse_uniref was called once with the config to produce the resource
-    mock_parse_uniref.assert_called_once_with(config)
+    # parse_uniref was called once with the settings to produce the resource
+    mock_parse_uniref.assert_called_once_with(test_settings)
 
-    # the return value of parse_uniref(config) is what gets passed to pipeline.run
+    # the return value of parse_uniref(settings) is what gets passed to pipeline.run
     expected_resource = mock_parse_uniref.return_value
 
-    mock_dlt.destination.assert_called_once_with(config.destination)
+    mock_dlt.destination.assert_called_once_with(test_settings.use_destination)
     mock_dlt.pipeline.assert_called_once_with(
         destination=mock_dlt.destination.return_value,
-        pipeline_name=f"uniref_{config.uniref_variant}",
+        pipeline_name=f"uniref_{test_settings.uniref_variant}",
         dataset_name="uniprot_kb",
     )
     mock_dlt.pipeline.return_value.run.assert_called_once_with(
@@ -223,24 +270,24 @@ def test_run_uniref_pipeline_sets_core_run_pipeline_args_correctly(
     )
 
 
-def test_parse_uniref_resource(config: Settings) -> None:
+def test_parse_uniref_resource(test_settings: UnirefSettings) -> None:
     """Ensure that parse_uniref calls stream_xml_file_resource with the namespaced UniRef XML tag."""
     with patch.object(uniref_module, "stream_xml_file_resource") as mock_stream:
         mock_stream.return_value = iter([])
-        list(parse_uniref(config))
+        list(parse_uniref(test_settings))
 
     assert mock_stream.call_count == 1
     kwargs = mock_stream.call_args.kwargs
-    assert kwargs.keys() == {"config", "xml_tag", "parse_fn", "log_interval"}
+    assert kwargs.keys() == {"settings", "xml_tag", "parse_fn", "log_interval"}
     assert kwargs["xml_tag"] == ENTRY_XML_TAG
     assert kwargs["log_interval"] == UNIREF_LOG_INTERVAL
-    assert kwargs["config"] == config
+    assert kwargs["settings"] == test_settings
     assert isinstance(kwargs["parse_fn"], Callable)
 
 
 @pytest.mark.skip("FIXME: not working -- due to parallelization?")
 def test_integration_cli_uniref_pipeline_output_validated(
-    config: Settings,  # parametrized over UNIREF_VARIANTS via the existing fixture
+    test_settings: UnirefSettings,  # parametrized over UNIREF_VARIANTS via the existing fixture
     fake_files: list[Path],
     mock_dlt: MagicMock,
     patched_io: tuple[MagicMock, MagicMock],
@@ -264,37 +311,37 @@ def fake_parse_uniref_entry(
     ) -> dict[str, list[Any]]:
         """Replacement for parse_uniref_entry; validates the injected label."""
         assert isinstance(timestamp, datetime.datetime)
-        assert uniref_variant == f"UniRef {config.uniref_variant}"
+        assert uniref_variant == f"UniRef {test_settings.uniref_variant}"
         assert entry == {"stream_xml_file": file_path, "xml_tag": ENTRY_XML_TAG}
         return {"entry": [entry], "file_path": [file_path]}
 
-    def fake_pipeline_run(resource, **kwargs) -> list:
+    def fake_pipeline_run(resource, **kwargs) -> list:  # noqa: ANN001, ANN003
         """Fake pipeline run that drains the resource generator to trigger all assertions."""
         assert isinstance(resource, Callable)  # after draining the generator, resource should be a list
-        assert resource.name == "parse_uniref"  # the resource should be the output of parse_uniref
+        # the resource should be the output of parse_uniref
+        assert resource.name == "parse_uniref"
         assert kwargs == {"table_format": "delta"}
-        output = list(resource)
-        return output
+        return list(resource)
 
     mock_stream.side_effect = fake_stream_xml_file
     monkeypatch.setattr(uniref_module, "parse_uniref_entry", fake_parse_uniref_entry)
 
     # make pipeline.run drain the generator so all assertions fire
-    # mock_dlt.pipeline.return_value.run.side_effect = lambda resource, **_: list(resource)
     mock_dlt.pipeline.return_value.run.side_effect = fake_pipeline_run
 
-    # exercise the real cli() wiring with Settings construction mocked out
-    monkeypatch.setattr(uniref_module, "Settings", MagicMock(return_value=config))
+    # exercise the real cli() wiring with UnirefSettings construction mocked out
+    monkeypatch.setattr(uniref_module, "UnirefSettings", MagicMock(return_value=test_settings))
 
     # RUN!
     cli()
 
     mock_dlt.pipeline.assert_called_once_with(
-        pipeline_name=f"uniref_{config.uniref_variant}",
-        destination=mock_dlt.destination.return_value,
+        pipeline_name=f"uniref_{test_settings.uniref_variant}",
+        use_destination=mock_dlt.use_destination.return_value,
         dataset_name="uniprot_kb",
+        dev_mode=False,
     )
-    mock_dlt.destination.assert_called_once_with(config.destination)
+    mock_dlt.use_destination.assert_called_once_with(test_settings.use_destination)
     mock_dlt.pipeline.return_value.run.assert_called_once()
 
     # verify with_table_name received the right rows and table names for every file, in order
diff --git a/tests/utils/download/test_clients.py b/tests/utils/download/test_clients.py
index 3be2460c..0bc8120b 100644
--- a/tests/utils/download/test_clients.py
+++ b/tests/utils/download/test_clients.py
@@ -3,6 +3,7 @@
 import hashlib
 import logging
 from pathlib import Path
+from unittest.mock import AsyncMock, MagicMock, patch
 
 import httpx
 import pytest
@@ -237,7 +238,8 @@ def handler(_: httpx.Request) -> httpx.Response:
     assert destination.read_bytes() == sample_content
 
 
-@pytest.mark.slow_test
+@patch("tenacity.nap.time.sleep", MagicMock())
+@patch("asyncio.sleep", AsyncMock())
 @pytest.mark.parametrize("max_attempts", range(1, 5))
 @pytest.mark.parametrize("response_type", ["error", "timeout"])
 @pytest.mark.asyncio
@@ -297,7 +299,8 @@ def handler_timeout(_: httpx.Request) -> httpx.Response:
         assert len(retry_possible_msgs) == successful_attempt - 1
 
 
-@pytest.mark.slow_test
+@patch("tenacity.nap.time.sleep", MagicMock())
+@patch("asyncio.sleep", AsyncMock())
 @pytest.mark.parametrize("max_attempts", range(1, 5))
 @pytest.mark.asyncio
 async def test_client_error_retries(
diff --git a/uv.lock b/uv.lock
index f133ae16..243a2da8 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
 version = 1
-revision = 2
+revision = 3
 requires-python = ">=3.13"
 resolution-markers = [
     "python_full_version >= '3.14' and platform_python_implementation != 'PyPy' and sys_platform != 'emscripten'",
@@ -14,7 +14,7 @@ resolution-markers = [
 
 [[package]]
 name = "aiobotocore"
-version = "3.2.0"
+version = "3.4.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohttp" },
@@ -25,9 +25,9 @@ dependencies = [
     { name = "python-dateutil" },
     { name = "wrapt" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/11/8d/5f155bdebd5b2acebb9432e64ae658d807c79b29d09308e020ce98b16ca3/aiobotocore-3.2.0.tar.gz", hash = "sha256:93e67b507d913bc168212f30a0e01e1835e07e665f00749fcac037e01999d72a", size = 122746, upload-time = "2026-02-24T15:23:57.368Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/b8/50/a48ed11b15f926ce3dbb33e7fb0f25af17dbb99bcb7ae3b30c763723eca7/aiobotocore-3.4.0.tar.gz", hash = "sha256:a918b5cb903f81feba7e26835aed4b5e6bb2d0149d7f42bb2dd7d8089e3d9000", size = 122360, upload-time = "2026-04-07T06:12:24.884Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/f6/df/5274db7c8a6f5b37d5053a3c9899b2e61964226f8f488294ae3c50825fd4/aiobotocore-3.2.0-py3-none-any.whl", hash = "sha256:7578eb807d2215f2c34d49a3986c821431af3c85ae9a464020ed91dff7925e2e", size = 87718, upload-time = "2026-02-24T15:23:55.713Z" },
+    { url = "https://files.pythonhosted.org/packages/df/d8/ce9386e6d76ea79e61dee15e62aa48cff6be69e89246b0ac4a11857cb02c/aiobotocore-3.4.0-py3-none-any.whl", hash = "sha256:26290eb6830ea92d8a6f5f90b56e9f5cedd6d126074d5db63b195e281d982465", size = 88018, upload-time = "2026-04-07T06:12:22.684Z" },
 ]
 
 [[package]]
@@ -41,7 +41,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.3"
+version = "3.13.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -52,59 +52,59 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/97/8a/12ca489246ca1faaf5432844adbfce7ff2cc4997733e0af120869345643a/aiohttp-3.13.3-cp313-cp313-macosx_10_13_universal2.whl", hash = "sha256:5dff64413671b0d3e7d5918ea490bdccb97a4ad29b3f311ed423200b2203e01c", size = 734190, upload-time = "2026-01-03T17:30:45.832Z" },
-    { url = "https://files.pythonhosted.org/packages/32/08/de43984c74ed1fca5c014808963cc83cb00d7bb06af228f132d33862ca76/aiohttp-3.13.3-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:87b9aab6d6ed88235aa2970294f496ff1a1f9adcd724d800e9b952395a80ffd9", size = 491783, upload-time = "2026-01-03T17:30:47.466Z" },
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