Merge branch 'dev' into fix-cache-path

.github/workflows/create-test-lint-wf-template.yml

@@ -152,6 +152,12 @@ jobs:
         run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned
         working-directory: create-test-lint-wf
 
+      # Run code style linting
+      - name: run pre-commit
+        shell: bash
+        run: pre-commit run --all-files
+        working-directory: create-test-lint-wf
+
       # Run bump-version
       - name: nf-core pipelines bump-version
         run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1

.github/workflows/pytest.yml

@@ -198,7 +198,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@b9fd7d16f6d7d1b5d2bec1a2887e65ceed900238 # v4
+      - uses: codecov/codecov-action@5c47607acb93fed5485fdbf7232e8a31425f672a # v5
         with:
           files: coverage.xml
         env:

.gitignore

@@ -113,7 +113,6 @@ ENV/
 # Jetbrains IDEs
 .idea
 pip-wheel-metadata
-.vscode
 .*.sw?
 
 # Textual

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.1
+    rev: v0.7.4
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -17,6 +17,8 @@
 
 ### Linting
 
+- General: Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+
 ### Modules
 
 - add a panel around diff previews when updating ([#3246](https://github.com/nf-core/tools/pull/3246))
@@ -36,6 +38,13 @@
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
 - Fix usage of cache path and implement parallized testing ([#3291](https://github.com/nf-core/tools/pull/3291))
+- handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
+- Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
+- Add hint to solve git errors with a synced repo ([#3279](https://github.com/nf-core/tools/pull/3279))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 ([#3282](https://github.com/nf-core/tools/pull/3282))
+- Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283))
+- Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:032c52613401895aa3d418a4c563d2d05f993bc3ecc065c8f4e2280978acd249
+FROM python:3.12-slim@sha256:2a6386ad2db20e7f55073f69a98d6da2cf9f168e05e7487d2670baeb9b7601c5
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

nf_core/gitpod/gitpod.Dockerfile

@@ -23,9 +23,9 @@ RUN apt-get update --quiet && \
     add-apt-repository -y ppa:apptainer/ppa && \
     apt-get update --quiet && \
     apt-get install --quiet --yes apptainer && \
-    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniconda3-latest-Linux-x86_64.sh && \
+    wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
+    rm Miniforge3-Linux-x86_64.sh && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 

nf_core/pipeline-template/.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}

nf_core/pipeline-template/conf/modules.config

@@ -18,13 +18,15 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    {% if fastqc -%}
+    {%- if fastqc %}
+
     withName: FASTQC {
         ext.args = '--quiet'
     }
     {%- endif %}
 
     {%- if multiqc %}
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

nf_core/pipeline-template/main.nf

@@ -109,8 +109,10 @@ workflow {
         {%- endif %}
         params.outdir,
         params.monochrome_logs,
-        {% if adaptivecard or slackreport %}params.hook_url,{% endif %}
-        {% if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
+        {%- if adaptivecard or slackreport %}
+        params.hook_url,{% endif %}
+        {%- if multiqc %}
+        {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
     {%- endif %}
 }

nf_core/pipeline-template/nextflow.config

@@ -13,39 +13,47 @@ params {
     // Input options
     input                      = null
 
-    {% if igenomes -%}
+    {%- if igenomes %}
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     {%- endif %}
 
-    {% if multiqc -%}
+    {%- if multiqc %}
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
-    {% if citations %}multiqc_methods_description = null{% endif %}
+    {%- if citations %}
+    multiqc_methods_description = null{% endif %}
     {%- endif %}
 
     // Boilerplate options
     outdir                       = null
-    {% if modules %}publish_dir_mode             = 'copy'{% endif %}
+    {%- if modules %}
+    publish_dir_mode             = 'copy'{% endif %}
     {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
     {%- endif %}
-    {% if modules %}monochrome_logs              = false{% endif %}
-    {% if slackreport or adaptivecard %}hook_url                     = null{% endif %}
-    {% if nf_schema %}help                         = false
+    {%- if modules %}
+    monochrome_logs              = false{% endif %}
+    {%- if slackreport or adaptivecard %}
+    hook_url                     = null{% endif %}
+    {%- if nf_schema %}
+    help                         = false
     help_full                    = false
     show_hidden                  = false{% endif %}
     version                      = false
-    {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
+    {%- if test_config %}
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
-    {% if nf_core_configs -%}
+    {%- if nf_core_configs -%}
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -56,7 +64,8 @@ params {
     config_profile_url         = null
     {%- endif %}
 
-    {% if nf_schema -%}
+    {%- if nf_schema %}
+
     // Schema validation default options
     validate_params            = true
     {%- endif %}
@@ -173,7 +182,7 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    {% if gitpod -%}
+    {%- if gitpod %}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
@@ -187,7 +196,7 @@ profiles {
         }
     }
     {%- endif %}
-    {% if test_config -%}
+    {%- if test_config %}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     {%- endif %}

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -128,8 +128,10 @@ workflow PIPELINE_COMPLETION {
     {%- endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    {% if adaptivecard or slackreport %}hook_url        //  string: hook URL for notifications{% endif %}
-    {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
+    {%- if adaptivecard or slackreport %}
+    hook_url        //  string: hook URL for notifications{% endif %}
+    {%- if multiqc %}
+    multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
     {%- if nf_schema %}
@@ -237,8 +239,10 @@ def toolCitationText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
-            {% if fastqc %}"FastQC (Andrews 2010),",{% endif %}
-            {% if multiqc %}"MultiQC (Ewels et al. 2016)",{% endif %}
+            {%- if fastqc %}
+            "FastQC (Andrews 2010),",{% endif %}
+            {%- if multiqc %}
+            "MultiQC (Ewels et al. 2016)",{% endif %}
             "."
         ].join(' ').trim()
 
@@ -250,8 +254,10 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            {% if fastqc %}"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",{% endif %}
-            {% if multiqc %}"<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"{% endif %}
+            {%- if fastqc %}
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",{% endif %}
+            {%- if multiqc %}
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"{% endif %}
         ].join(' ').trim()
 
     return reference_text

nf_core/pipeline-template/workflows/pipeline.nf

@@ -5,12 +5,17 @@
 */
 
 {%- if modules %}
-{% if fastqc %}include { FASTQC                 } from '../modules/nf-core/fastqc/main'{% endif %}
-{% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-{% if nf_schema %}include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
-{% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
+{%- if fastqc %}
+include { FASTQC                 } from '../modules/nf-core/fastqc/main'{% endif %}
+{%- if multiqc %}
+include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
+{%- if nf_schema %}
+include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
+{%- if multiqc %}
+include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-{% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+{%- if citations or multiqc %}
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 {%- endif %}
 
 /*
@@ -28,7 +33,8 @@ workflow {{ short_name|upper }} {
     main:
 
     ch_versions = Channel.empty()
-    {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
+    {%- if multiqc %}
+    ch_multiqc_files = Channel.empty(){% endif %}
 
     {%- if fastqc %}
     //

nf_core/pipelines/create/template_features.yml

@@ -432,3 +432,14 @@ seqera_platform:
     You can extend this file adding any other desired configuration.
   nfcore_pipelines: False
   custom_pipelines: True
+vscode:
+  skippable_paths:
+    - ".vscode"
+  short_description: "Render website admonitions in VSCode"
+  description: "Add a VSCode configuration to render website admonitions"
+  help_text: |
+    This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website.
+
+    Adds the `.vscode` directory to the pipelinerepository.
+  nfcore_pipelines: False
+  custom_pipelines: True