From 7f1b7d781d922a21766d050b24e593b661e18a44 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 25 Mar 2026 18:55:41 +0100
Subject: [PATCH 01/10] adding modules for downloading and running gguf modules

---
 .../huggingface/download/environment.yml      |   6 +
 modules/nf-core/huggingface/download/main.nf  |  30 ++++
 modules/nf-core/huggingface/download/meta.yml |  60 ++++++++
 .../huggingface/download/tests/main.nf.test   |  64 ++++++++
 .../download/tests/main.nf.test.snap          |  34 +++++
 .../nf-core/llamacpp-python/run/Dockerfile    |   5 +
 .../llamacpp-python/run/environment.yml       |   7 +
 modules/nf-core/llamacpp-python/run/main.nf   |  36 +++++
 modules/nf-core/llamacpp-python/run/meta.yml  |  50 +++++++
 .../run/resources/usr/bin/llamacpp-python.py  | 137 ++++++++++++++++++
 .../run/tests/data/prompt.json                |  11 ++
 .../run/tests/data/stub_model.gguf            |   0
 .../llamacpp-python/run/tests/main.nf.test    |  79 ++++++++++
 .../run/tests/main.nf.test.snap               |  34 +++++
 .../llamacpp-python/run/tests/nextflow.config |   7 +
 15 files changed, 560 insertions(+)
 create mode 100644 modules/nf-core/huggingface/download/environment.yml
 create mode 100644 modules/nf-core/huggingface/download/main.nf
 create mode 100644 modules/nf-core/huggingface/download/meta.yml
 create mode 100644 modules/nf-core/huggingface/download/tests/main.nf.test
 create mode 100644 modules/nf-core/huggingface/download/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/llamacpp-python/run/Dockerfile
 create mode 100644 modules/nf-core/llamacpp-python/run/environment.yml
 create mode 100644 modules/nf-core/llamacpp-python/run/main.nf
 create mode 100644 modules/nf-core/llamacpp-python/run/meta.yml
 create mode 100755 modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
 create mode 100644 modules/nf-core/llamacpp-python/run/tests/data/prompt.json
 create mode 100644 modules/nf-core/llamacpp-python/run/tests/data/stub_model.gguf
 create mode 100644 modules/nf-core/llamacpp-python/run/tests/main.nf.test
 create mode 100644 modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/llamacpp-python/run/tests/nextflow.config

diff --git a/modules/nf-core/huggingface/download/environment.yml b/modules/nf-core/huggingface/download/environment.yml
new file mode 100644
index 000000000000..f2267b412f67
--- /dev/null
+++ b/modules/nf-core/huggingface/download/environment.yml
@@ -0,0 +1,6 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+dependencies:
+  - conda-forge::huggingface_hub=1.6.0
diff --git a/modules/nf-core/huggingface/download/main.nf b/modules/nf-core/huggingface/download/main.nf
new file mode 100644
index 000000000000..50e389afb415
--- /dev/null
+++ b/modules/nf-core/huggingface/download/main.nf
@@ -0,0 +1,30 @@
+process HF_DOWNLOAD {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/huggingface_hub:1.6.0--c106a7f9664ca39b"
+
+    input:
+    tuple val(meta), val(hf_repo), val(hf_file)
+
+    output:
+    tuple val(meta), path(hf_file), emit: output
+    tuple val("${task.process}"), val("huggingface_hub"), eval("hf --version 2>&1"), topic: versions, emit: versions_huggingface_hub
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    export HF_HOME="${workflow.projectDir}/hf_cache"
+    export HF_HUB_CACHE="${workflow.projectDir}/hf_cache"
+    STARTDIR=\$PWD
+    hf download ${hf_repo} ${hf_file} --local-dir \$STARTDIR
+    """
+
+    stub:
+    """
+    touch ${hf_file}
+    """
+}
diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
new file mode 100644
index 000000000000..c9a5abe83fe4
--- /dev/null
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -0,0 +1,60 @@
+name: huggignface_hub
+description: Tool for downloading models from HuggingFace
+keywords:
+  - llm
+  - llama
+  - ai
+tools:
+  - huggignface_hub:
+      description: "HuggingFace Hub CLI interface"
+      homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
+      licence: ["MIT"]
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`- prompt_file:
+    - hf_repo:
+        type: string
+        description: HuggingFace repository
+    - hf_file:
+        type: string
+        description: HuggingFace GGUF file
+output:
+  output:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - output:
+          type: file
+          description: Model in GGUF format
+          pattern: "*.gguf"
+  versions_huggingface_hub:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - huggingface_hub:
+          type: string
+          description: The name of the tool
+      - hf --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@toniher"
+  - "@lucacozzuto"
+maintainers:
+  - "@toniher"
+  - "@lucacozzuto"
diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test b/modules/nf-core/huggingface/download/tests/main.nf.test
new file mode 100644
index 000000000000..b15446029a9c
--- /dev/null
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test
@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process HF_DOWNLOAD"
+    script "../main.nf"
+    process "HF_DOWNLOAD"
+
+    tag "modules"
+    tag "modules_local"
+    tag "huggingface"
+    tag "huggingface/download"
+
+    test("download gguf file") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_model' ],
+                    "ggml-org/gemma-3-1b-it-GGUF",
+                    "gemma-3-1b-it-Q4_K_M.gguf"
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.output.size() == 1 },
+                { assert process.out.output[0][0] == [ id:'test_model' ] },
+                { assert file(process.out.output[0][1]).name == "gemma-3-1b-it-Q4_K_M.gguf" },
+                { assert file(process.out.output[0][1]).size() > 0 },
+                { assert snapshot(process.out.versions_huggingface_hub).match() }
+            )
+        }
+    }
+
+    test("stub - download gguf file") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_model' ],
+                    "ggml-org/gemma-3-1b-it-GGUF",
+                    "gemma-3-1b-it-Q4_K_M.gguf"
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.output.size() == 1 },
+                { assert process.out.output[0][0] == [ id:'test_model' ] },
+                { assert file(process.out.output[0][1]).name == "gemma-3-1b-it-Q4_K_M.gguf" },
+                { assert snapshot(process.out.versions_huggingface_hub).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test.snap b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
new file mode 100644
index 000000000000..fb0ec0f4e827
--- /dev/null
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
@@ -0,0 +1,34 @@
+{
+    "stub - download gguf file": {
+        "content": [
+            [
+                [
+                    "HF_DOWNLOAD",
+                    "huggingface_hub",
+                    "1.6.0"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-25T17:55:42.821958238",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "download gguf file": {
+        "content": [
+            [
+                [
+                    "HF_DOWNLOAD",
+                    "huggingface_hub",
+                    "1.6.0"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-25T17:55:36.08739868",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/llamacpp-python/run/Dockerfile b/modules/nf-core/llamacpp-python/run/Dockerfile
new file mode 100644
index 000000000000..aeb89834ee1c
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/Dockerfile
@@ -0,0 +1,5 @@
+FROM nvidia/cuda:12.4.1-devel-ubuntu22.04
+
+RUN apt-get update && apt-get install -y python3 python3-pip
+RUN pip3 install llama-cpp-python  \
+    --extra-index-url https://abetlen.github.io/llama-cpp-python/whl/cu124
diff --git a/modules/nf-core/llamacpp-python/run/environment.yml b/modules/nf-core/llamacpp-python/run/environment.yml
new file mode 100644
index 000000000000..9f314201924a
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::llama-cpp-python=0.3.16
diff --git a/modules/nf-core/llamacpp-python/run/main.nf b/modules/nf-core/llamacpp-python/run/main.nf
new file mode 100644
index 000000000000..5dec0f6bcf28
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/main.nf
@@ -0,0 +1,36 @@
+process LLAMACPP_PYTHON_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'process_gpu'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ task.ext.use_gpu ? 'quay.io/nf-core/llama-cpp-python:0.1.9' : 'community.wave.seqera.io/library/llama-cpp-python:0.3.16--b351398cd0ea7fc5' }"
+
+    input:
+    tuple val(meta), path(prompt_file), path(gguf_model)
+
+    output:
+    tuple val(meta), path("output.txt"), emit: output
+    tuple val("${task.process}"), val("llama-cpp-python"), eval("python3 -c 'import llama_cpp; print(llama_cpp.__version__)'"), topic: versions, emit: versions_llama_cpp_python
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    llamacpp-python.py \
+        --model ${gguf_model} \
+        --messages ${prompt_file} \
+        --output output.txt \
+        ${args}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch output.txt
+
+    """
+}
diff --git a/modules/nf-core/llamacpp-python/run/meta.yml b/modules/nf-core/llamacpp-python/run/meta.yml
new file mode 100644
index 000000000000..15f4b893829b
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/meta.yml
@@ -0,0 +1,50 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: llamacpp-python
+description: Python wrapper for running locally-hosted LLM with llama.cpp
+keywords:
+  - llm
+  - llama
+  - ai
+input:
+  - prompt_file:
+      type: file
+      description: |
+        Prompt file
+        Structure: [ val(meta), path(prompt_file) ]
+  - gguf_model:
+      type: file
+      description: |
+        GGUF model
+        Structure: [ val(meta), path(gguf_model) ]
+output:
+  - output:
+      type: file
+      description: |
+        Output of the LLM query
+        Structure: [ val(meta), path("output.txt") ]
+      pattern: "output.txt"
+  - versions_llama_cpp_python:
+      type: file
+      description: |
+        File containing software versions
+        Structure: path(versions.yml)
+      pattern: "versions.yml"
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - llama-cpp-python:
+          type: string
+          description: The name of the tool
+      - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@toniher"
+  - "@lucacozzuto"
+maintainers:
+  - "@toniher"
+  - "@lucacozzuto"
+
diff --git a/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py b/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
new file mode 100755
index 000000000000..e9e6123544f3
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
@@ -0,0 +1,137 @@
+#!/usr/bin/env python3
+
+import argparse
+import json
+import os
+import sys
+
+import llama_cpp
+
+
+# Helper to create messages from a text file
+def create_messages_from_textfile(textfile, system_prompt):
+    try:
+        with open(textfile, "r", encoding="utf-8") as f:
+            content = f.read()
+        return [
+            {"role": "system", "content": system_prompt.strip()},
+            {"role": "user", "content": content.strip()},
+        ]
+    except Exception as e:
+        print(f"Error reading text file '{textfile}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+# Helper to load messages from JSON or fallback to text
+def load_messages(messages_file, system_prompt):
+    if not os.path.exists(messages_file):
+        print(f"Messages file '{messages_file}' does not exist.", file=sys.stderr)
+        sys.exit(1)
+    try:
+        with open(messages_file, "r", encoding="utf-8") as f:
+            content = f.read()
+            try:
+                return json.loads(content)
+            except json.JSONDecodeError:
+                return create_messages_from_textfile(messages_file, system_prompt)
+    except Exception as e:
+        print(f"Error opening messages file '{messages_file}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+def llamacpp_python(
+    messages_file,
+    model_file,
+    temperature=0.9,
+    output="output.txt",
+    verbose=False,
+    context_size=2048,
+    chat_format="chatml",
+    seed=None,
+):
+    if not os.path.exists(model_file):
+        print(f"Model file '{model_file}' does not exist.", file=sys.stderr)
+        sys.exit(1)
+
+    # Default system prompt
+    system_prompt = "A chat between a curious user and an artificial intelligence assistant. The assistant gives helpful, detailed, and polite answers to the user's questions"
+
+    messages_json = load_messages(messages_file, system_prompt)
+
+    try:
+        llm = llama_cpp.Llama(
+            model_path=model_file,
+            chat_format=chat_format,
+            n_ctx=context_size,
+            seed=seed,
+        )
+        response = llm.create_chat_completion(
+            messages=messages_json,
+            response_format={"type": "json_object"},
+            temperature=temperature,
+        )
+    except Exception as e:
+        print(f"Error running llama_cpp: {e}", file=sys.stderr)
+        sys.exit(1)
+
+    if not verbose:
+        try:
+            reply = response["choices"][0]["message"]["content"]
+        except (KeyError, IndexError, TypeError):
+            reply = response
+        # Try to parse reply as JSON if it's a string
+        if isinstance(reply, str):
+            try:
+                reply_json = json.loads(reply)
+                if isinstance(reply_json, dict) and len(reply_json) == 1:
+                    reply = next(iter(reply_json.values()))
+                else:
+                    reply = reply_json
+            except Exception:
+                pass  # Leave reply as string if not valid JSON
+        elif isinstance(reply, dict) and len(reply) == 1:
+            reply = next(iter(reply.values()))
+    else:
+        reply = response
+
+    try:
+        with open(output, "w", encoding="utf-8") as f:
+            if isinstance(reply, str):
+                f.write(reply)
+            else:
+                f.write(json.dumps(reply, indent=2))
+        if verbose:
+            print(f"Output written to {output}")
+    except Exception as e:
+        print(f"Error writing output file '{output}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Submit a process with model.")
+    parser.add_argument("-s", "--messages", required=True, help="JSON message")
+    parser.add_argument("-m", "--model", required=True, help="Model used")
+    parser.add_argument(
+        "-t", "--temperature", default=0.9, type=float, help="Temperature"
+    )
+    parser.add_argument("-o", "--output", default="output.txt", help="Output text")
+    parser.add_argument("-c", "--context", default=2048, type=int, help="Context size")
+    parser.add_argument("--chat_format", default="chatml", help="Chat format")
+    parser.add_argument("--seed", default=None, type=int, help="Defined seed")
+    parser.add_argument("--verbose", action="store_true", help="Verbose output")
+
+    args = parser.parse_args()
+    llamacpp_python(
+        messages_file=args.messages,
+        model_file=args.model,
+        temperature=args.temperature,
+        output=args.output,
+        verbose=args.verbose,
+        context_size=args.context,
+        chat_format=args.chat_format,
+        seed=args.seed,
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/llamacpp-python/run/tests/data/prompt.json b/modules/nf-core/llamacpp-python/run/tests/data/prompt.json
new file mode 100644
index 000000000000..7d76ad158bab
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/tests/data/prompt.json
@@ -0,0 +1,11 @@
+[
+    {
+        "role": "system",
+        "content": "A chat between a curious user and an artificial intelligence assistant. The assistant gives helpful, detailed, and polite answers to the user's questions"
+
+    },
+    {
+        "role": "user",
+        "content": "Describe Barcelona in one paragraph"
+    }
+]
diff --git a/modules/nf-core/llamacpp-python/run/tests/data/stub_model.gguf b/modules/nf-core/llamacpp-python/run/tests/data/stub_model.gguf
new file mode 100644
index 000000000000..e69de29bb2d1
diff --git a/modules/nf-core/llamacpp-python/run/tests/main.nf.test b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
new file mode 100644
index 000000000000..a3483d6dc9dc
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process LLAMACPP_PYTHON_RUN"
+    script "../main.nf"
+    process "LLAMACPP_PYTHON_RUN"
+
+    tag "modules"
+    tag "modules_local"
+    tag "llamacpp_python"
+    tag "llamacpp_python/run"
+
+    test("run inference with downloaded gguf model") {
+
+        config "./nextflow.config"
+
+        setup {
+            run("HF_DOWNLOAD") {
+                script "../../../huggingface/download/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test_model' ],
+                        "ggml-org/gemma-3-1b-it-GGUF",
+                        "gemma-3-1b-it-Q4_K_M.gguf"
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = HF_DOWNLOAD.out.output.map { meta, model ->
+                    [ [ id:'test_run' ], file("${moduleDir}/tests/data/prompt.json"), model ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.output.size() == 1 },
+                { assert process.out.output[0][0] == [ id:'test_run' ] },
+                { assert file(process.out.output[0][1]).name == "output.txt" },
+                { assert file(process.out.output[0][1]).size() > 0 },
+                { assert snapshot(process.out.versions_llama_cpp_python).match() }
+            )
+        }
+    }
+
+    test("stub - run inference with json prompt") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ],
+                    file("${moduleDir}/tests/data/prompt.json"),
+                    file("${moduleDir}/tests/data/stub_model.gguf")
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.output.size() == 1 },
+                { assert process.out.output[0][0] == [ id:'test_run' ] },
+                { assert file(process.out.output[0][1]).name == "output.txt" },
+                { assert snapshot(process.out.versions_llama_cpp_python).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap b/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
new file mode 100644
index 000000000000..5f5b167f758b
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
@@ -0,0 +1,34 @@
+{
+    "run inference with downloaded gguf model": {
+        "content": [
+            [
+                [
+                    "LLAMACPP_PYTHON_RUN",
+                    "llama-cpp-python",
+                    "0.3.16"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-25T18:33:08.596485421",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "stub - run inference with json prompt": {
+        "content": [
+            [
+                [
+                    "LLAMACPP_PYTHON_RUN",
+                    "llama-cpp-python",
+                    "0.3.16"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-25T17:23:21.997786726",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/llamacpp-python/run/tests/nextflow.config b/modules/nf-core/llamacpp-python/run/tests/nextflow.config
new file mode 100644
index 000000000000..7a6b3c247728
--- /dev/null
+++ b/modules/nf-core/llamacpp-python/run/tests/nextflow.config
@@ -0,0 +1,7 @@
+nextflow.enable.moduleBinaries = true
+
+process {
+    withName: 'LLAMACPP_PYTHON_RUN' {
+        ext.args = "--seed 42"
+    }
+}

From 9031f483a189cd2ce880a9eb0fe8b178cd2c99e6 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 25 Mar 2026 19:33:59 +0100
Subject: [PATCH 02/10] adding docker support

---
 modules/nf-core/huggingface/download/tests/nextflow.config | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 modules/nf-core/huggingface/download/tests/nextflow.config

diff --git a/modules/nf-core/huggingface/download/tests/nextflow.config b/modules/nf-core/huggingface/download/tests/nextflow.config
new file mode 100644
index 000000000000..68a5630f57cb
--- /dev/null
+++ b/modules/nf-core/huggingface/download/tests/nextflow.config
@@ -0,0 +1,7 @@
+nextflow.enable.moduleBinaries = true
+
+process {
+    withName: 'HF_DOWNLOAD' {
+        containerOptions = { workflow.profile.contains('docker') ? "--volume ${projectDir}/hf_cache:${projectDir}/hf_cache" : '' }
+    }
+}

From 04cd556c9a722501fc3c68403240433008e25c4e Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 08:46:54 +0100
Subject: [PATCH 03/10] allow custom HF_HOME cache input and other fixes

---
 modules/nf-core/huggingface/download/main.nf         | 12 ++++++------
 modules/nf-core/huggingface/download/meta.yml        |  2 +-
 .../nf-core/huggingface/download/tests/main.nf.test  |  6 ++++--
 .../huggingface/download/tests/main.nf.test.snap     |  4 ++--
 4 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/huggingface/download/main.nf b/modules/nf-core/huggingface/download/main.nf
index 50e389afb415..63eef3a5bcb2 100644
--- a/modules/nf-core/huggingface/download/main.nf
+++ b/modules/nf-core/huggingface/download/main.nf
@@ -6,21 +6,21 @@ process HF_DOWNLOAD {
     container "community.wave.seqera.io/library/huggingface_hub:1.6.0--c106a7f9664ca39b"
 
     input:
-    tuple val(meta), val(hf_repo), val(hf_file)
+    tuple val(meta), val(hf_repo), val(hf_file), val(hf_home)
 
     output:
     tuple val(meta), path(hf_file), emit: output
-    tuple val("${task.process}"), val("huggingface_hub"), eval("hf --version 2>&1"), topic: versions, emit: versions_huggingface_hub
+    tuple val("${task.process}"), val("huggingface_hub"), eval("hf --version 2>&1 | awk '{print \$NF}'"), topic: versions, emit: versions_huggingface_hub
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def hf_home_resolved = hf_home ?: "${workflow.projectDir}/hf_cache"
     """
-    export HF_HOME="${workflow.projectDir}/hf_cache"
-    export HF_HUB_CACHE="${workflow.projectDir}/hf_cache"
-    STARTDIR=\$PWD
-    hf download ${hf_repo} ${hf_file} --local-dir \$STARTDIR
+    export HF_HOME="${hf_home_resolved}"
+    export HF_HUB_CACHE=\$HF_HOME
+    hf download ${hf_repo} ${hf_file} --local-dir \$PWD
     """
 
     stub:
diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
index c9a5abe83fe4..8c8332a879e5 100644
--- a/modules/nf-core/huggingface/download/meta.yml
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -50,7 +50,7 @@ topics:
           description: The name of the tool
       - hf --version:
           type: eval
-          description: The expression to obtain the version of the tool
+          description: The expression to obtain only the version number of the tool (e.g. "1.6.0")
 
 authors:
   - "@toniher"
diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test b/modules/nf-core/huggingface/download/tests/main.nf.test
index b15446029a9c..94d0112862c4 100644
--- a/modules/nf-core/huggingface/download/tests/main.nf.test
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test
@@ -17,7 +17,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test_model' ],
                     "ggml-org/gemma-3-1b-it-GGUF",
-                    "gemma-3-1b-it-Q4_K_M.gguf"
+                    "gemma-3-1b-it-Q4_K_M.gguf",
+                    "./hf_cache"
                 ]
                 """
             }
@@ -45,7 +46,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test_model' ],
                     "ggml-org/gemma-3-1b-it-GGUF",
-                    "gemma-3-1b-it-Q4_K_M.gguf"
+                    "gemma-3-1b-it-Q4_K_M.gguf",
+                    "./hf_cache"
                 ]
                 """
             }
diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test.snap b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
index fb0ec0f4e827..406face5c7a6 100644
--- a/modules/nf-core/huggingface/download/tests/main.nf.test.snap
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
@@ -9,7 +9,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-25T17:55:42.821958238",
+        "timestamp": "2026-03-26T08:39:57.919278809",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -25,7 +25,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-25T17:55:36.08739868",
+        "timestamp": "2026-03-26T08:38:24.630341776",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From 537a891ef8b6dbd7ef7962131e0305a39a2acd3d Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 10:12:38 +0100
Subject: [PATCH 04/10] several test fixes

---
 modules/nf-core/huggingface/download/meta.yml | 98 ++++++++++---------
 modules/nf-core/llamacpp-python/run/meta.yml  | 83 ++++++++++------
 2 files changed, 103 insertions(+), 78 deletions(-)

diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
index 8c8332a879e5..f540eb08b6c3 100644
--- a/modules/nf-core/huggingface/download/meta.yml
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -1,60 +1,66 @@
-name: huggignface_hub
+name: hf_download
 description: Tool for downloading models from HuggingFace
 keywords:
-  - llm
-  - llama
-  - ai
+- llm
+- llama
+- ai
 tools:
-  - huggignface_hub:
-      description: "HuggingFace Hub CLI interface"
-      homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
-      licence: ["MIT"]
+- huggingface_hub:
+    description: "HuggingFace Hub CLI interface"
+    homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
+    licence:
+    - "MIT"
+    identifier: ''
 input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`- prompt_file:
+  - hf_repo:
+      type: string
+      description: HuggingFace repository
+  - hf_file:
+      type: string
+      description: HuggingFace GGUF file
+  - hf_home:
+      type: string
+      description: HuggingFace default cache directory
+output:
+  output:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1' ]`- prompt_file:
-    - hf_repo:
-        type: string
-        description: HuggingFace repository
+          e.g. `[ id:'sample1' ]`
     - hf_file:
-        type: string
-        description: HuggingFace GGUF file
-output:
-  output:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1' ]`
-      - output:
-          type: file
-          description: Model in GGUF format
-          pattern: "*.gguf"
-  versions_huggingface_hub:
-    - versions.yml:
         type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
-
+        description: Downloaded HuggingFace GGUF file
+        ontologies: []
+  versions_huggingface_hub:
+  - - ${task.process}:
+        type: string
+        description: The name of the process
+    - huggingface_hub:
+        type: string
+        description: The name of the tool
+    - hf --version 2>&1 | awk '{print \$NF}':
+        type: eval
+        description: The expression to obtain the version of the tool
 topics:
   versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - huggingface_hub:
-          type: string
-          description: The name of the tool
-      - hf --version:
-          type: eval
-          description: The expression to obtain only the version number of the tool (e.g. "1.6.0")
-
+  - - ${task.process}:
+        type: string
+        description: The name of the process
+    - huggingface_hub:
+        type: string
+        description: The name of the tool
+    - hf --version 2>&1 | awk '{print \$NF}':
+        type: eval
+        description: The expression to obtain the version of the tool
 authors:
-  - "@toniher"
-  - "@lucacozzuto"
+- "@toniher"
+- "@lucacozzuto"
 maintainers:
-  - "@toniher"
-  - "@lucacozzuto"
+- "@toniher"
+- "@lucacozzuto"
diff --git a/modules/nf-core/llamacpp-python/run/meta.yml b/modules/nf-core/llamacpp-python/run/meta.yml
index 15f4b893829b..18607a776271 100644
--- a/modules/nf-core/llamacpp-python/run/meta.yml
+++ b/modules/nf-core/llamacpp-python/run/meta.yml
@@ -1,50 +1,69 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: llamacpp-python
+name: llamacpp_python_run
 description: Python wrapper for running locally-hosted LLM with llama.cpp
 keywords:
-  - llm
-  - llama
-  - ai
+- llm
+- llama
+- ai
+tools:
+- llama-cpp-python:
+    description: "Python wrapper for llama.cpp LLM inference tool"
+    homepage: "https://llama-cpp-python.readthedocs.io/en/latest/"
+    licence:
+    - "MIT"
+    identifier: ''
 input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`- prompt_file:
   - prompt_file:
       type: file
       description: |
         Prompt file
         Structure: [ val(meta), path(prompt_file) ]
+      ontologies: []
   - gguf_model:
       type: file
       description: |
         GGUF model
         Structure: [ val(meta), path(gguf_model) ]
+      ontologies: []
 output:
-  - output:
-      type: file
-      description: |
-        Output of the LLM query
-        Structure: [ val(meta), path("output.txt") ]
-      pattern: "output.txt"
-  - versions_llama_cpp_python:
-      type: file
-      description: |
-        File containing software versions
-        Structure: path(versions.yml)
-      pattern: "versions.yml"
-
+  output:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - "output.txt":
+        type: file
+        description: File with the output of LLM inference request
+        ontologies: []
+  versions_llama_cpp_python:
+  - - ${task.process}:
+        type: string
+        description: The name of the process
+    - llama-cpp-python:
+        type: string
+        description: The name of the tool
+    - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
+        type: eval
+        description: The expression to obtain the version of the tool
 topics:
   versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - llama-cpp-python:
-          type: string
-          description: The name of the tool
-      - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
-          type: eval
-          description: The expression to obtain the version of the tool
+  - - ${task.process}:
+        type: string
+        description: The name of the process
+    - llama-cpp-python:
+        type: string
+        description: The name of the tool
+    - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
+        type: eval
+        description: The expression to obtain the version of the tool
 authors:
-  - "@toniher"
-  - "@lucacozzuto"
+- "@toniher"
+- "@lucacozzuto"
 maintainers:
-  - "@toniher"
-  - "@lucacozzuto"
-
+- "@toniher"
+- "@lucacozzuto"

From 20b5d26348c628747268de179fefab024d450300 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 11:54:03 +0100
Subject: [PATCH 05/10] Upgrade problem with versions and test

---
 .../huggingface/download/tests/main.nf.test   |  6 ++--
 .../download/tests/main.nf.test.snap          | 30 +++++++++++--------
 .../llamacpp-python/run/tests/main.nf.test    | 11 +++----
 .../run/tests/main.nf.test.snap               | 30 +++++++++++--------
 4 files changed, 43 insertions(+), 34 deletions(-)

diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test b/modules/nf-core/huggingface/download/tests/main.nf.test
index 94d0112862c4..2173c5d32897 100644
--- a/modules/nf-core/huggingface/download/tests/main.nf.test
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "HF_DOWNLOAD"
 
     tag "modules"
-    tag "modules_local"
+    tag "modules_nfcore"
     tag "huggingface"
     tag "huggingface/download"
 
@@ -31,7 +31,7 @@ nextflow_process {
                 { assert process.out.output[0][0] == [ id:'test_model' ] },
                 { assert file(process.out.output[0][1]).name == "gemma-3-1b-it-Q4_K_M.gguf" },
                 { assert file(process.out.output[0][1]).size() > 0 },
-                { assert snapshot(process.out.versions_huggingface_hub).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -59,7 +59,7 @@ nextflow_process {
                 { assert process.out.output.size() == 1 },
                 { assert process.out.output[0][0] == [ id:'test_model' ] },
                 { assert file(process.out.output[0][1]).name == "gemma-3-1b-it-Q4_K_M.gguf" },
-                { assert snapshot(process.out.versions_huggingface_hub).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
diff --git a/modules/nf-core/huggingface/download/tests/main.nf.test.snap b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
index 406face5c7a6..5565340150b6 100644
--- a/modules/nf-core/huggingface/download/tests/main.nf.test.snap
+++ b/modules/nf-core/huggingface/download/tests/main.nf.test.snap
@@ -1,13 +1,15 @@
 {
     "stub - download gguf file": {
         "content": [
-            [
-                [
-                    "HF_DOWNLOAD",
-                    "huggingface_hub",
-                    "1.6.0"
+            {
+                "versions_huggingface_hub": [
+                    [
+                        "HF_DOWNLOAD",
+                        "huggingface_hub",
+                        "1.6.0"
+                    ]
                 ]
-            ]
+            }
         ],
         "timestamp": "2026-03-26T08:39:57.919278809",
         "meta": {
@@ -17,13 +19,15 @@
     },
     "download gguf file": {
         "content": [
-            [
-                [
-                    "HF_DOWNLOAD",
-                    "huggingface_hub",
-                    "1.6.0"
+            {
+                "versions_huggingface_hub": [
+                    [
+                        "HF_DOWNLOAD",
+                        "huggingface_hub",
+                        "1.6.0"
+                    ]
                 ]
-            ]
+            }
         ],
         "timestamp": "2026-03-26T08:38:24.630341776",
         "meta": {
@@ -31,4 +35,4 @@
             "nextflow": "25.10.4"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/llamacpp-python/run/tests/main.nf.test b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
index a3483d6dc9dc..469ce2d8d258 100644
--- a/modules/nf-core/llamacpp-python/run/tests/main.nf.test
+++ b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
@@ -5,9 +5,10 @@ nextflow_process {
     process "LLAMACPP_PYTHON_RUN"
 
     tag "modules"
-    tag "modules_local"
-    tag "llamacpp_python"
-    tag "llamacpp_python/run"
+    tag "modules_nfcore"
+    tag "llamacpp-python"
+    tag "llamacpp-python/run"
+    tag "huggingface/download"
 
     test("run inference with downloaded gguf model") {
 
@@ -45,7 +46,7 @@ nextflow_process {
                 { assert process.out.output[0][0] == [ id:'test_run' ] },
                 { assert file(process.out.output[0][1]).name == "output.txt" },
                 { assert file(process.out.output[0][1]).size() > 0 },
-                { assert snapshot(process.out.versions_llama_cpp_python).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -72,7 +73,7 @@ nextflow_process {
                 { assert process.out.output.size() == 1 },
                 { assert process.out.output[0][0] == [ id:'test_run' ] },
                 { assert file(process.out.output[0][1]).name == "output.txt" },
-                { assert snapshot(process.out.versions_llama_cpp_python).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
diff --git a/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap b/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
index 5f5b167f758b..4bd263f10e6e 100644
--- a/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
+++ b/modules/nf-core/llamacpp-python/run/tests/main.nf.test.snap
@@ -1,13 +1,15 @@
 {
     "run inference with downloaded gguf model": {
         "content": [
-            [
-                [
-                    "LLAMACPP_PYTHON_RUN",
-                    "llama-cpp-python",
-                    "0.3.16"
+            {
+                "versions_llama_cpp_python": [
+                    [
+                        "LLAMACPP_PYTHON_RUN",
+                        "llama-cpp-python",
+                        "0.3.16"
+                    ]
                 ]
-            ]
+            }
         ],
         "timestamp": "2026-03-25T18:33:08.596485421",
         "meta": {
@@ -17,13 +19,15 @@
     },
     "stub - run inference with json prompt": {
         "content": [
-            [
-                [
-                    "LLAMACPP_PYTHON_RUN",
-                    "llama-cpp-python",
-                    "0.3.16"
+            {
+                "versions_llama_cpp_python": [
+                    [
+                        "LLAMACPP_PYTHON_RUN",
+                        "llama-cpp-python",
+                        "0.3.16"
+                    ]
                 ]
-            ]
+            }
         ],
         "timestamp": "2026-03-25T17:23:21.997786726",
         "meta": {
@@ -31,4 +35,4 @@
             "nextflow": "25.10.4"
         }
     }
-}
\ No newline at end of file
+}

From c9997f53e502cd3dbf35b47a370512260adc9877 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 12:27:15 +0100
Subject: [PATCH 06/10] fix precommit linting

---
 modules/nf-core/huggingface/download/meta.yml | 26 +++++++++----------
 modules/nf-core/llamacpp-python/run/meta.yml  | 26 +++++++++----------
 .../run/resources/usr/bin/llamacpp-python.py  |  8 +++---
 .../run/tests/data/prompt.json                |  1 -
 4 files changed, 29 insertions(+), 32 deletions(-)

diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
index f540eb08b6c3..b3512b4ea075 100644
--- a/modules/nf-core/huggingface/download/meta.yml
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -1,16 +1,16 @@
 name: hf_download
 description: Tool for downloading models from HuggingFace
 keywords:
-- llm
-- llama
-- ai
+  - llm
+  - llama
+  - ai
 tools:
-- huggingface_hub:
-    description: "HuggingFace Hub CLI interface"
-    homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
-    licence:
-    - "MIT"
-    identifier: ''
+  - huggingface_hub:
+      description: "HuggingFace Hub CLI interface"
+      homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
+      licence:
+      - "MIT"
+      identifier: ''
 input:
 - - meta:
       type: map
@@ -59,8 +59,8 @@ topics:
         type: eval
         description: The expression to obtain the version of the tool
 authors:
-- "@toniher"
-- "@lucacozzuto"
+  - "@toniher"
+  - "@lucacozzuto"
 maintainers:
-- "@toniher"
-- "@lucacozzuto"
+  - "@toniher"
+  - "@lucacozzuto"
diff --git a/modules/nf-core/llamacpp-python/run/meta.yml b/modules/nf-core/llamacpp-python/run/meta.yml
index 18607a776271..bd8ca208a075 100644
--- a/modules/nf-core/llamacpp-python/run/meta.yml
+++ b/modules/nf-core/llamacpp-python/run/meta.yml
@@ -1,16 +1,16 @@
 name: llamacpp_python_run
 description: Python wrapper for running locally-hosted LLM with llama.cpp
 keywords:
-- llm
-- llama
-- ai
+  - llm
+  - llama
+  - ai
 tools:
-- llama-cpp-python:
-    description: "Python wrapper for llama.cpp LLM inference tool"
-    homepage: "https://llama-cpp-python.readthedocs.io/en/latest/"
-    licence:
-    - "MIT"
-    identifier: ''
+  - llama-cpp-python:
+      description: "Python wrapper for llama.cpp LLM inference tool"
+      homepage: "https://llama-cpp-python.readthedocs.io/en/latest/"
+      licence:
+      - "MIT"
+      identifier: ''
 input:
 - - meta:
       type: map
@@ -62,8 +62,8 @@ topics:
         type: eval
         description: The expression to obtain the version of the tool
 authors:
-- "@toniher"
-- "@lucacozzuto"
+  - "@toniher"
+  - "@lucacozzuto"
 maintainers:
-- "@toniher"
-- "@lucacozzuto"
+  - "@toniher"
+  - "@lucacozzuto"
diff --git a/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py b/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
index e9e6123544f3..4e332bca6338 100755
--- a/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
+++ b/modules/nf-core/llamacpp-python/run/resources/usr/bin/llamacpp-python.py
@@ -11,7 +11,7 @@
 # Helper to create messages from a text file
 def create_messages_from_textfile(textfile, system_prompt):
     try:
-        with open(textfile, "r", encoding="utf-8") as f:
+        with open(textfile, encoding="utf-8") as f:
             content = f.read()
         return [
             {"role": "system", "content": system_prompt.strip()},
@@ -28,7 +28,7 @@ def load_messages(messages_file, system_prompt):
         print(f"Messages file '{messages_file}' does not exist.", file=sys.stderr)
         sys.exit(1)
     try:
-        with open(messages_file, "r", encoding="utf-8") as f:
+        with open(messages_file, encoding="utf-8") as f:
             content = f.read()
             try:
                 return json.loads(content)
@@ -111,9 +111,7 @@ def main():
     parser = argparse.ArgumentParser(description="Submit a process with model.")
     parser.add_argument("-s", "--messages", required=True, help="JSON message")
     parser.add_argument("-m", "--model", required=True, help="Model used")
-    parser.add_argument(
-        "-t", "--temperature", default=0.9, type=float, help="Temperature"
-    )
+    parser.add_argument("-t", "--temperature", default=0.9, type=float, help="Temperature")
     parser.add_argument("-o", "--output", default="output.txt", help="Output text")
     parser.add_argument("-c", "--context", default=2048, type=int, help="Context size")
     parser.add_argument("--chat_format", default="chatml", help="Chat format")
diff --git a/modules/nf-core/llamacpp-python/run/tests/data/prompt.json b/modules/nf-core/llamacpp-python/run/tests/data/prompt.json
index 7d76ad158bab..52d9ea3e2aa7 100644
--- a/modules/nf-core/llamacpp-python/run/tests/data/prompt.json
+++ b/modules/nf-core/llamacpp-python/run/tests/data/prompt.json
@@ -2,7 +2,6 @@
     {
         "role": "system",
         "content": "A chat between a curious user and an artificial intelligence assistant. The assistant gives helpful, detailed, and polite answers to the user's questions"
-
     },
     {
         "role": "user",

From 5035e82beb3af788cde1960e79d607d99e7e7686 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 13:08:09 +0100
Subject: [PATCH 07/10] fix yaml for prettier

---
 modules/nf-core/huggingface/download/meta.yml | 78 ++++++++---------
 modules/nf-core/llamacpp-python/run/meta.yml  | 84 +++++++++----------
 2 files changed, 81 insertions(+), 81 deletions(-)

diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
index b3512b4ea075..9ca5bed5d613 100644
--- a/modules/nf-core/huggingface/download/meta.yml
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -9,55 +9,55 @@ tools:
       description: "HuggingFace Hub CLI interface"
       homepage: "https://huggingface.co/docs/huggingface_hub/guides/cli"
       licence:
-      - "MIT"
-      identifier: ''
+        - "MIT"
+      identifier: ""
 input:
-- - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1' ]`- prompt_file:
-  - hf_repo:
-      type: string
-      description: HuggingFace repository
-  - hf_file:
-      type: string
-      description: HuggingFace GGUF file
-  - hf_home:
-      type: string
-      description: HuggingFace default cache directory
-output:
-  output:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1' ]`
+          e.g. `[ id:'sample1' ]`- prompt_file:
+    - hf_repo:
+        type: string
+        description: HuggingFace repository
     - hf_file:
-        type: file
-        description: Downloaded HuggingFace GGUF file
-        ontologies: []
-  versions_huggingface_hub:
-  - - ${task.process}:
         type: string
-        description: The name of the process
-    - huggingface_hub:
+        description: HuggingFace GGUF file
+    - hf_home:
         type: string
-        description: The name of the tool
-    - hf --version 2>&1 | awk '{print \$NF}':
-        type: eval
-        description: The expression to obtain the version of the tool
+        description: HuggingFace default cache directory
+output:
+  output:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - hf_file:
+          type: file
+          description: Downloaded HuggingFace GGUF file
+          ontologies: []
+  versions_huggingface_hub:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - huggingface_hub:
+          type: string
+          description: The name of the tool
+      - hf --version 2>&1 | awk '{print \$NF}':
+          type: eval
+          description: The expression to obtain the version of the tool
 topics:
   versions:
-  - - ${task.process}:
-        type: string
-        description: The name of the process
-    - huggingface_hub:
-        type: string
-        description: The name of the tool
-    - hf --version 2>&1 | awk '{print \$NF}':
-        type: eval
-        description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - huggingface_hub:
+          type: string
+          description: The name of the tool
+      - hf --version 2>&1 | awk '{print \$NF}':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@toniher"
   - "@lucacozzuto"
diff --git a/modules/nf-core/llamacpp-python/run/meta.yml b/modules/nf-core/llamacpp-python/run/meta.yml
index bd8ca208a075..70d7bbf4f162 100644
--- a/modules/nf-core/llamacpp-python/run/meta.yml
+++ b/modules/nf-core/llamacpp-python/run/meta.yml
@@ -9,58 +9,58 @@ tools:
       description: "Python wrapper for llama.cpp LLM inference tool"
       homepage: "https://llama-cpp-python.readthedocs.io/en/latest/"
       licence:
-      - "MIT"
-      identifier: ''
+        - "MIT"
+      identifier: ""
 input:
-- - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1' ]`- prompt_file:
-  - prompt_file:
-      type: file
-      description: |
-        Prompt file
-        Structure: [ val(meta), path(prompt_file) ]
-      ontologies: []
-  - gguf_model:
-      type: file
-      description: |
-        GGUF model
-        Structure: [ val(meta), path(gguf_model) ]
-      ontologies: []
-output:
-  output:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1' ]`
-    - "output.txt":
+          e.g. `[ id:'sample1' ]`- prompt_file:
+    - prompt_file:
+        type: file
+        description: |
+          Prompt file
+          Structure: [ val(meta), path(prompt_file) ]
+        ontologies: []
+    - gguf_model:
         type: file
-        description: File with the output of LLM inference request
+        description: |
+          GGUF model
+          Structure: [ val(meta), path(gguf_model) ]
         ontologies: []
+output:
+  output:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "output.txt":
+          type: file
+          description: File with the output of LLM inference request
+          ontologies: []
   versions_llama_cpp_python:
-  - - ${task.process}:
-        type: string
-        description: The name of the process
-    - llama-cpp-python:
-        type: string
-        description: The name of the tool
-    - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
-        type: eval
-        description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - llama-cpp-python:
+          type: string
+          description: The name of the tool
+      - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
 topics:
   versions:
-  - - ${task.process}:
-        type: string
-        description: The name of the process
-    - llama-cpp-python:
-        type: string
-        description: The name of the tool
-    - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
-        type: eval
-        description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - llama-cpp-python:
+          type: string
+          description: The name of the tool
+      - python3 -c 'import llama_cpp; print(llama_cpp.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@toniher"
   - "@lucacozzuto"

From 2c796de96acc5514afcb7924758686d1d952bcc8 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 13:44:02 +0100
Subject: [PATCH 08/10] fix retrieval of version for huggingface

---
 modules/nf-core/huggingface/download/main.nf  | 2 +-
 modules/nf-core/huggingface/download/meta.yml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/huggingface/download/main.nf b/modules/nf-core/huggingface/download/main.nf
index 63eef3a5bcb2..78c6211ac34f 100644
--- a/modules/nf-core/huggingface/download/main.nf
+++ b/modules/nf-core/huggingface/download/main.nf
@@ -10,7 +10,7 @@ process HF_DOWNLOAD {
 
     output:
     tuple val(meta), path(hf_file), emit: output
-    tuple val("${task.process}"), val("huggingface_hub"), eval("hf --version 2>&1 | awk '{print \$NF}'"), topic: versions, emit: versions_huggingface_hub
+    tuple val("${task.process}"), val("huggingface_hub"), eval("hf --version 2>&1 | tail -n1 | awk '{print \$NF}'"), topic: versions, emit: versions_huggingface_hub
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/huggingface/download/meta.yml b/modules/nf-core/huggingface/download/meta.yml
index 9ca5bed5d613..a3186bce7b07 100644
--- a/modules/nf-core/huggingface/download/meta.yml
+++ b/modules/nf-core/huggingface/download/meta.yml
@@ -44,7 +44,7 @@ output:
       - huggingface_hub:
           type: string
           description: The name of the tool
-      - hf --version 2>&1 | awk '{print \$NF}':
+      - hf --version 2>&1 | tail -n1 | awk '{print \$NF}':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -55,7 +55,7 @@ topics:
       - huggingface_hub:
           type: string
           description: The name of the tool
-      - hf --version 2>&1 | awk '{print \$NF}':
+      - hf --version 2>&1 | tail -n1 | awk '{print \$NF}':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

From ff7039c53d6010eea6b8d94d7bf084820c2fb86f Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 14:02:28 +0100
Subject: [PATCH 09/10] importing nextflow.config from HF_DOWNLOAD

---
 modules/nf-core/llamacpp-python/run/tests/nextflow.config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/nf-core/llamacpp-python/run/tests/nextflow.config b/modules/nf-core/llamacpp-python/run/tests/nextflow.config
index 7a6b3c247728..6806a86ca3ef 100644
--- a/modules/nf-core/llamacpp-python/run/tests/nextflow.config
+++ b/modules/nf-core/llamacpp-python/run/tests/nextflow.config
@@ -1,6 +1,9 @@
 nextflow.enable.moduleBinaries = true
 
 process {
+    withName: 'HF_DOWNLOAD' {
+        containerOptions = { workflow.profile.contains('docker') ? "--volume ${projectDir}/hf_cache:${projectDir}/hf_cache" : '' }
+    }
     withName: 'LLAMACPP_PYTHON_RUN' {
         ext.args = "--seed 42"
     }

From fb1768c4e6621e3abcf993da4e532c35051ab796 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Thu, 26 Mar 2026 14:51:46 +0100
Subject: [PATCH 10/10] adding hf_cache for setup as well

---
 modules/nf-core/llamacpp-python/run/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/llamacpp-python/run/tests/main.nf.test b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
index 469ce2d8d258..dc789505242d 100644
--- a/modules/nf-core/llamacpp-python/run/tests/main.nf.test
+++ b/modules/nf-core/llamacpp-python/run/tests/main.nf.test
@@ -22,7 +22,8 @@ nextflow_process {
                     input[0] = [
                         [ id:'test_model' ],
                         "ggml-org/gemma-3-1b-it-GGUF",
-                        "gemma-3-1b-it-Q4_K_M.gguf"
+                        "gemma-3-1b-it-Q4_K_M.gguf",
+                        "./hf_cache"
                     ]
                     """
                 }