Template: add option to exclude the workflows directory from pipeline template

CHANGELOG.md

@@ -38,6 +38,7 @@
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 - run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
+- add option to exclude the workflows directory from pipeline template ([#3170](https://github.com/nf-core/tools/pull/3170))
 
 ### Linting
 

nf_core/pipeline-template/main.nf

@@ -17,7 +17,18 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+{%- if workflows_dir %}
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
+{%- else %}
+{%- 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 %}
+include { softwareVersionsToYAML  } from './subworkflows/nf-core/utils_nfcore_pipeline'
+{% if citations or multiqc %}include { methodsDescriptionText  } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+{%- endif %}
+{%- endif %}
 {%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
@@ -49,17 +60,93 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     take:
     samplesheet // channel: samplesheet read in from --input
 
+{% if workflows_dir %}
     main:
-
     //
     // WORKFLOW: Run pipeline
     //
     {{ short_name|upper }} (
         samplesheet
     )
+{% else %}
+    {%- if modules %}
+    main:
+    ch_versions = Channel.empty()
+    {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
+
+    {%- if fastqc %}
+    //
+    // MODULE: Run FastQC
+    //
+    FASTQC (
+        samplesheet
+    )
+    {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %}
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    {%- endif %}
+
+    //
+    // Collate and save software versions
+    //
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
+
+    {% if multiqc %}
+    //
+    // MODULE: MultiQC
+    //
+    ch_multiqc_config        = Channel.fromPath(
+        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ?
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.empty()
+    ch_multiqc_logo          = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    {% if nf_schema %}
+    summary_params      = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    {% endif %}
+
+    {%- if citations %}
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+    {%- endif %}
+
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    {%- if citations %}
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: true
+        )
+    )
+    {%- endif %}
+
+    MULTIQC (
+        ch_multiqc_files.collect(),
+        ch_multiqc_config.toList(),
+        ch_multiqc_custom_config.toList(),
+        ch_multiqc_logo.toList()
+    )
+    {%- endif %}
+    {%- endif %}
+{%- endif %}
 {%- if multiqc %}{%- if modules %}
     emit:
-    multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
+    multiqc_report = {% if workflows_dir %}{{ short_name|upper }}.out.multiqc_report{% else %}MULTIQC.out.report.toList(){% endif %} // channel: /path/to/multiqc_report.html
 {%- endif %}{%- endif %}
 }
 /*

nf_core/pipelines/create/template_features.yml

@@ -272,6 +272,18 @@ modules:
       - "modules.json"
   nfcore_pipelines: False
   custom_pipelines: True
+workflows_dir:
+  skippable_paths:
+    - "workflows"
+  short_description: "Add workflows directory"
+  description: "Add a directory to store Nextflow workflows"
+  help_text: |
+    This will add a directory to store Nextflow workflows.
+    This is useful to keep the pipeline structure clean and organized.
+
+    The pipeline structure will have a `main.nf` file in the root directory. This will contain the main workflow and call the rest of the workflows in the `workflows` directory.
+  nfcore_pipelines: False
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"