Merge pull request #3406 from nf-core/dev

dev -> main for 3.1.2

Author: mirpedrol

.github/workflows/sync.yml

@@ -97,7 +97,7 @@ jobs:
 
         run: |
           pushd nf-core/${{ matrix.pipeline }}
-          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2 | sed "s/'//g")
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
           fi

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.8.6
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -19,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.13.0"
+    rev: "v1.14.1"
     hooks:
       - id: mypy
         additional_dependencies:

CHANGELOG.md

@@ -1,5 +1,28 @@
 # nf-core/tools: Changelog
 
+## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]
+
+### Template
+
+- Bump nf-schema to `2.3.0` ([#3401](https://github.com/nf-core/tools/pull/3401))
+- Remove jinja formatting which was deleting line breaks ([#3405](https://github.com/nf-core/tools/pull/3405))
+
+### Download
+
+- Allow `nf-core pipelines download -r` to download commits ([#3374](https://github.com/nf-core/tools/pull/3374))
+- Fix faulty Download Test Action to ensure that setup and test run as one job and on the same runner ([#3389](https://github.com/nf-core/tools/pull/3389))
+
+### Modules
+
+- Fix bump-versions: only append module name if it is a dir and contains `main.nf` ([#3384](https://github.com/nf-core/tools/pull/3384))
+
+### General
+
+- `manifest.author` is not required anymore ([#3397](https://github.com/nf-core/tools/pull/3397))
+- Parameters schema validation: allow `oneOf`, `anyOf` and `allOf` with `required` ([#3386](https://github.com/nf-core/tools/pull/3386))
+- Run pre-comit when rendering template for pipelines sync ([#3371](https://github.com/nf-core/tools/pull/3371))
+- Fix sync GHA by removing quotes from parsed branch name ([#3394](https://github.com/nf-core/tools/pull/3394))
+
 ## [v3.1.1 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.1) - [2024-12-20]
 
 ### Template

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:2b0079146a74e23bf4ae8f6a28e1b484c6292f6fb904cbb51825b4a19812fcd8
+FROM python:3.12-slim@sha256:10f3aaab98db50cba827d3b33a91f39dc9ec2d02ca9b85cbc5008220d07b17f3
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

nf_core/modules/modules_utils.py

@@ -65,19 +65,20 @@ def get_installed_modules(directory: Path, repo_type="modules") -> Tuple[List[st
             local_modules = sorted([x for x in local_modules if x.endswith(".nf")])
 
     # Get nf-core modules
-    if os.path.exists(nfcore_modules_dir):
-        for m in sorted([m for m in os.listdir(nfcore_modules_dir) if not m == "lib"]):
-            if not os.path.isdir(os.path.join(nfcore_modules_dir, m)):
+    if nfcore_modules_dir.exists():
+        for m in sorted([m for m in nfcore_modules_dir.iterdir() if not m == "lib"]):
+            if not m.is_dir():
                 raise ModuleExceptionError(
                     f"File found in '{nfcore_modules_dir}': '{m}'! This directory should only contain module directories."
                 )
-            m_content = os.listdir(os.path.join(nfcore_modules_dir, m))
+            m_content = [d.name for d in m.iterdir()]
             # Not a module, but contains sub-modules
             if "main.nf" not in m_content:
                 for tool in m_content:
-                    nfcore_modules_names.append(os.path.join(m, tool))
+                    if (m / tool).is_dir() and "main.nf" in [d.name for d in (m / tool).iterdir()]:
+                        nfcore_modules_names.append(str(Path(m.name, tool)))
             else:
-                nfcore_modules_names.append(m)
+                nfcore_modules_names.append(m.name)
 
     # Make full (relative) file paths and create NFCoreComponent objects
     if local_modules_dir:

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -46,6 +46,8 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -35,7 +35,18 @@ jobs:
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
     steps:
-      - name: Install Nextflow{% endraw %}
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
+    steps:
+      - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
@@ -56,24 +67,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        id: get_repo_properties
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
-  download:
-    runs-on: ubuntu-latest
-    needs: configure
-    steps:
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %}
         run: |
           nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
           --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
@@ -85,7 +85,10 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %}
 
       - name: Count the downloaded number of container images
         id: count_initial
@@ -123,7 +126,8 @@ jobs:
             final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"

nf_core/pipeline-template/CITATIONS.md

@@ -18,7 +18,7 @@
 
 {%- endif %}
 
-{%- if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 

nf_core/pipeline-template/README.md

@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{%- else -%}
+{% else -%}
 
 # {{ name }}
 
@@ -54,7 +54,7 @@
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {%- if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -120,7 +120,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use {{ name }} for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-{%- if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+{% if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 {%- endif %}

nf_core/pipeline-template/conf/test.config

@@ -27,7 +27,8 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    {% if igenomes -%}
+    {%- if igenomes -%}
+
     // Genome references
     genome = 'R64-1-1'
     {%- endif %}

nf_core/pipeline-template/nextflow.config

@@ -295,7 +295,7 @@ manifest {
 {% if nf_schema -%}
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

nf_core/pipelines/create/create.py

@@ -386,6 +386,10 @@ def render_template(self) -> None:
                     yaml.dump(config_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper())
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
+        # Run prettier on files for pipelines sync
+        log.debug("Running prettier on pipeline files")
+        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+
     def fix_linting(self):
         """
         Updates the .nf-core.yml with linting configurations

nf_core/pipelines/download.py

@@ -374,30 +374,37 @@ def prompt_revision(self) -> None:
                     raise AssertionError(f"No revisions of {self.pipeline} available for download.")
 
     def get_revision_hash(self):
-        """Find specified revision / branch hash"""
+        """Find specified revision / branch / commit hash"""
 
         for revision in self.revision:  # revision is a list of strings, but may be of length 1
             # Branch
             if revision in self.wf_branches.keys():
                 self.wf_sha = {**self.wf_sha, revision: self.wf_branches[revision]}
 
-            # Revision
             else:
+                # Revision
                 for r in self.wf_revisions:
                     if r["tag_name"] == revision:
                         self.wf_sha = {**self.wf_sha, revision: r["tag_sha"]}
                         break
 
-                # Can't find the revisions or branch - throw an error
                 else:
+                    # Commit - full or short hash
+                    if commit_id := nf_core.utils.get_repo_commit(self.pipeline, revision):
+                        self.wf_sha = {**self.wf_sha, revision: commit_id}
+                        continue
+
+                    # Can't find the revisions or branch - throw an error
                     log.info(
                         "Available {} revisions: '{}'".format(
                             self.pipeline,
                             "', '".join([r["tag_name"] for r in self.wf_revisions]),
                         )
                     )
                     log.info("Available {} branches: '{}'".format(self.pipeline, "', '".join(self.wf_branches.keys())))
-                    raise AssertionError(f"Not able to find revision / branch '{revision}' for {self.pipeline}")
+                    raise AssertionError(
+                        f"Not able to find revision / branch / commit '{revision}' for {self.pipeline}"
+                    )
 
         # Set the outdir
         if not self.outdir:
@@ -1536,7 +1543,7 @@ def singularity_pull_image(
 
         progress.remove_task(task)
 
-    def compress_download(self) -> None:
+    def compress_download(self):
         """Take the downloaded files and make a compressed .tar.gz archive."""
         log.debug(f"Creating archive: {self.output_filename}")
 

nf_core/pipelines/lint/files_unchanged.py

@@ -1,6 +1,7 @@
 import filecmp
 import logging
 import os
+import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -68,7 +69,10 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     could_fix: bool = False
 
     # Check that we have the minimum required config
-    required_pipeline_config = {"manifest.name", "manifest.description", "manifest.author"}
+    required_pipeline_config = {
+        "manifest.name",
+        "manifest.description",
+    }  # TODO: add "manifest.contributors" when minimum nextflow version is >=24.10.0
     missing_pipeline_config = required_pipeline_config.difference(self.nf_config)
     if missing_pipeline_config:
         return {"ignored": [f"Required pipeline config not found - {missing_pipeline_config}"]}
@@ -117,10 +121,15 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     tmp_dir.mkdir(parents=True)
 
     # Create a template.yaml file for the pipeline creation
+    if "manifest.author" in self.nf_config:
+        names = self.nf_config["manifest.author"].strip("\"'")
+    if "manifest.contributors" in self.nf_config:
+        contributors = self.nf_config["manifest.contributors"]
+        names = ", ".join(re.findall(r"name:'([^']+)'", contributors))
     template_yaml = {
         "name": short_name,
         "description": self.nf_config["manifest.description"].strip("\"'"),
-        "author": self.nf_config["manifest.author"].strip("\"'"),
+        "author": names,
         "org": prefix,
     }
 

nf_core/pipelines/lint_utils.py

@@ -70,6 +70,15 @@ def print_fixes(lint_obj):
         )
 
 
+def check_git_repo() -> bool:
+    """Check if the current directory is a git repository."""
+    try:
+        subprocess.check_output(["git", "rev-parse", "--is-inside-work-tree"])
+        return True
+    except subprocess.CalledProcessError:
+        return False
+
+
 def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None:
     """Run the pre-commit hook prettier on a file.
 
@@ -80,28 +89,33 @@ def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None:
         If Prettier is not installed, a warning is logged.
     """
 
+    is_git = check_git_repo()
+
     nf_core_pre_commit_config = Path(nf_core.__file__).parent / ".pre-commit-prettier-config.yaml"
     args = ["pre-commit", "run", "--config", str(nf_core_pre_commit_config), "prettier"]
     if isinstance(file, List):
         args.extend(["--files", *file])
     else:
         args.extend(["--files", str(file)])
 
-    try:
-        subprocess.run(args, capture_output=True, check=True)
-        log.debug(f"${subprocess.STDOUT}")
-    except subprocess.CalledProcessError as e:
-        if ": SyntaxError: " in e.stdout.decode():
-            log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
-        elif "files were modified by this hook" in e.stdout.decode():
-            all_lines = [line for line in e.stdout.decode().split("\n")]
-            files = "\n".join(all_lines[3:])
-            log.debug(f"The following files were modified by prettier:\n {files}")
-        else:
-            log.warning(
-                "There was an error running the prettier pre-commit hook.\n"
-                f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
-            )
+    if is_git:
+        try:
+            proc = subprocess.run(args, capture_output=True, check=True)
+            log.debug(f"{proc.stdout.decode()}")
+        except subprocess.CalledProcessError as e:
+            if ": SyntaxError: " in e.stdout.decode():
+                log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
+            elif "files were modified by this hook" in e.stdout.decode():
+                all_lines = [line for line in e.stdout.decode().split("\n")]
+                files = "\n".join(all_lines[3:])
+                log.debug(f"The following files were modified by prettier:\n {files}")
+            else:
+                log.warning(
+                    "There was an error running the prettier pre-commit hook.\n"
+                    f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
+                )
+    else:
+        log.debug("Not in a git repository, skipping pre-commit hook.")
 
 
 def dump_json_with_prettier(file_name, file_content):

nf_core/pipelines/rocrate.py

@@ -287,7 +287,7 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
         try:
             git_contributors: Set[str] = set()
             if self.pipeline_obj.repo is None:
-                log.info("No git repository found. No git contributors will be added as authors.")
+                log.debug("No git repository found. No git contributors will be added as authors.")
                 return
             commits_touching_path = list(self.pipeline_obj.repo.iter_commits(paths="main.nf"))