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mirpedrolmirpedrol
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Merge pull request #3280 from mirpedrol/run-pre-commit-with-lint-tests
General: Run pre-commit when testing linting the template pipeline
2 parents 0848508 + 269af7d commit d26c3e9

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

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

‎CHANGELOG.md‎

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@@ -17,6 +17,8 @@
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### Linting
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- General: Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
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### Modules
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- add a panel around diff previews when updating ([#3246](https://github.com/nf-core/tools/pull/3246))

‎nf_core/pipeline-template/conf/modules.config‎

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

‎nf_core/pipeline-template/main.nf‎

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

‎nf_core/pipeline-template/nextflow.config‎

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

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

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

‎nf_core/pipeline-template/workflows/pipeline.nf‎

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

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