Merge branch 'dev' into version-badges

.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

CHANGELOG.md

@@ -1,30 +1,41 @@
 # nf-core/tools: Changelog
 
-## v3.1.2dev
+## v3.2.0dev
 
 ### Template
 
 - Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396))
 
+### Linting
+
+### Modules
+
+### Subworkflows
+
+### General
+
+## [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))
 
-### Linting
-
 ### 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))
-
-### Subworkflows
+- 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
 
-- Parameters schema validation: allow oneOf, anyOf and allOf with `required` ([#3386](https://github.com/nf-core/tools/pull/3386))
+- `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))
-
-### Version updates
+- 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]
 

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 }}
 
@@ -55,7 +55,7 @@
 ## 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):
@@ -121,7 +121,7 @@ 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/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/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/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"))
 

nf_core/pipelines/sync.py

@@ -81,7 +81,11 @@ def __init__(
         self.made_changes = False
         self.make_pr = make_pr
         self.gh_pr_returned_data: Dict = {}
-        self.required_config_vars = ["manifest.name", "manifest.description", "manifest.version", "manifest.author"]
+        self.required_config_vars = [
+            "manifest.name",
+            "manifest.description",
+            "manifest.version",
+        ]  # TODO: add "manifest.contributors" when minimum nextflow version is >=24.10.0
         self.force_pr = force_pr
 
         self.gh_username = gh_username

nf_core/utils.py

@@ -1352,8 +1352,10 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
             contributors = wf_config["manifest.contributors"]
             names = re.findall(r"name:'([^']+)'", contributors)
             author_names = ", ".join(names)
-        else:
+        elif "manifest.author" in wf_config:
             author_names = wf_config["manifest.author"].strip("'\"")
+        else:
+            author_names = None
         if nf_core_yaml_config.template is None:
             # The .nf-core.yml file did not contain template information
             nf_core_yaml_config.template = NFCoreTemplateConfig(

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.1.2dev"
+version = "3.2.0dev"
 
 with open("README.md") as f:
     readme = f.read()