diff --git a/CHANGELOG.md b/CHANGELOG.md index e03aa90..fbea56d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,20 @@ # denoising devel +## NEW FUNCTIONALITY + * Add new method: CellMapper (PR #31) + +## MINOR CHANGES + +* Update the Viash version to 0.9.4 (PR #32) + +* Dependencies were moved to main openproblems repository (PR #32) + +## BUG FIXES + * Update scPRINT, including a new default model (PR #26) + # denoising v1.0.0 ## BREAKING CHANGES diff --git a/_viash.yaml b/_viash.yaml index 52f215f..1d5b436 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -3,6 +3,8 @@ organization: openproblems-bio version: dev license: MIT +viash_version: 0.9.4 + label: Denoising keywords: [single-cell, openproblems, benchmark, denoising] summary: "Removing noise in sparse single-cell RNA-sequencing count data" @@ -80,14 +82,12 @@ authors: info: github: marius1311 orcid: 0000-0002-4846-1266 + repositories: - - name: core + - name: openproblems type: github - repo: openproblems-bio/core + repo: openproblems-bio/openproblems tag: build/main - path: viash/core - -viash_version: 0.9.0 config_mods: | .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" } diff --git a/common b/common index 65e05af..79b884b 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 65e05af68a11ee87853fcf7a3c6b579001f21abe +Subproject commit 79b884b4c7fed300972d83a6ca025abb6116cbdc diff --git a/scripts/run_benchmark/run_full_seqeracloud.sh b/scripts/run_benchmark/run_full_seqeracloud.sh index 5508e37..defc77a 100755 --- a/scripts/run_benchmark/run_full_seqeracloud.sh +++ b/scripts/run_benchmark/run_full_seqeracloud.sh @@ -10,7 +10,7 @@ set -e # generate a unique id RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" -publish_dir="s3://openproblems-data/resources/task_denoising/results/${RUN_ID}" +publish_dir="s3://openproblems-data/resources/results/${RUN_ID}" # write the parameters to file cat > /tmp/params.yaml << HERE @@ -21,11 +21,10 @@ publish_dir: "$publish_dir" HERE tw launch https://github.com/openproblems-bio/task_denoising.git \ - --revision v1.0.0 \ + --revision build/main \ --pull-latest \ --main-script target/nextflow/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 5DwwhQoBi0knMSGcwThnlF \ --params-file /tmp/params.yaml \ --entry-name auto \ --config common/nextflow_helpers/labels_tw.config \ diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index 7d98b4b..cd27cd1 100644 --- a/src/workflows/process_datasets/config.vsh.yaml +++ b/src/workflows/process_datasets/config.vsh.yaml @@ -23,8 +23,8 @@ resources: entrypoint: run_wf - path: /common/nextflow_helpers/helper.nf dependencies: - - name: schema/verify_data_structure - repository: core + - name: validation/check_dataset_with_schema + repository: openproblems - name: data_processors/process_dataset runners: - type: nextflow diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf index 8b21d78..b1aec20 100644 --- a/src/workflows/process_datasets/main.nf +++ b/src/workflows/process_datasets/main.nf @@ -14,7 +14,7 @@ workflow run_wf { main: output_ch = input_ch - | verify_data_structure.run( + | check_dataset_with_schema.run( fromState: { id, state -> def schema = findArgumentSchema(meta.config, "input") def schemaYaml = tempFile("schema.yaml") diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index 996f623..292007b 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -67,8 +67,8 @@ resources: - path: /common/nextflow_helpers/helper.nf dependencies: - - name: h5ad/extract_uns_metadata - repository: core + - name: utils/extract_uns_metadata + repository: openproblems - name: control_methods/no_denoising - name: control_methods/perfect_denoising - name: methods/alra