Merge pull request #3280 from mirpedrol/run-pre-commit-with-lint-tests

General: Run pre-commit when testing linting the template pipeline
nf-core · Nov 14, 2024 · d26c3e9 · d26c3e9
2 parents 0848508 + 269af7d
commit d26c3e9
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Showing 7 changed files with 60 additions and 27 deletions.
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.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

diff --git a/CHANGELOG.md b/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))

diff --git a/nf_core/pipeline-template/conf/modules.config b/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 = [

diff --git a/nf_core/pipeline-template/main.nf b/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 %}
 }

diff --git a/nf_core/pipeline-template/nextflow.config b/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 %}

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/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

diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/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 %}
     //