Add (customisable) 'method description' MultiQC section to pipeline template

CHANGELOG.md

@@ -13,6 +13,7 @@
 - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
 - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729))
 - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728))
+- Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications
 
 ### Linting
 

nf_core/pipeline-template/assets/methods_description_template.yml

@@ -0,0 +1,25 @@
+id: "${workflow.manifest.name.replace('/', '-')}-methods-description"
+description: "Suggested methods description text of pipeline usage"
+section_name: "${ workflow.manifest.name } Methods Description"
+section_href: "https://github.com/${workflow.manifest.name}"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+  <b>Methods</b>
+  <p>Data was processed using the ${workflow.manifest.name} (v${workflow.manifest.version}, doi: ${workflow.manifest.doi}) of the nf-core collection of workflows (Ewels et al. 2020).</p>
+  <p>The pipeline was executed with Nextflow (v${workflow.nextflow.version}; Di Tommaso et al. 2017) with the following command:</p>
+  <pre><code>${workflow.commandLine}</code></pre>
+  <b>References</b>
+  <ul>
+  <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820 </li>
+  <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x </li>
+  </ul>
+  <blockquote>
+  <b>Notes:</b><br>
+  <ul>
+  <li>If present, make sure to replace the pipeline DOI with correct reference information.</li>
+  <li>The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+  <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+  </ul>
+  </blockquote>

nf_core/pipeline-template/assets/multiqc_config.yml

@@ -3,9 +3,11 @@ report_comment: >
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}" target="_blank">documentation</a>.{% endif %}
 report_section_order:
-  software_versions:
+  "{{ name.lower().replace('/', '-') }}-methods-description":
     order: -1000
-  "{{ name.lower().replace('/', '-') }}-summary":
+  software_versions:
     order: -1001
+  "{{ name.lower().replace('/', '-') }}-summary":
+    order: -1002
 
 export_plots: true

nf_core/pipeline-template/lib/WorkflowPipeline.groovy

@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/{{ short_name }}.nf in the {{ name }} pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
 
     //
@@ -45,6 +47,19 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
         return yaml_file_text
     }
 
+    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+        def meta = [:]
+        meta.workflow = run_workflow.toMap()
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
+    }
+
     {%- if igenomes -%}
     //
     // Exit pipeline if incorrect --genome key provided

nf_core/pipeline-template/nextflow.config

@@ -21,9 +21,10 @@ params {
     {% endif -%}
 
     // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    max_multiqc_email_size     = '25.MB'
+    multiqc_config              = null
+    multiqc_title               = null
+    max_multiqc_email_size      = '25.MB'
+    multiqc_methods_description = null
 
     // Boilerplate options
     outdir                     = null
@@ -191,6 +192,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
     version         = '{{ version }}'
+    doi             = ''
 }
 
 // Load modules.config for DSL2 module specific options

nf_core/pipeline-template/nextflow_schema.json

@@ -219,6 +219,12 @@
                     "fa_icon": "fas fa-cog",
                     "hidden": true
                 },
+                "multiqc_methods_description": {
+                    "type": "string",
+                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
+                    "fa_icon": "fas fa-cog",
+                    "hidden": true
+                },
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",

nf_core/pipeline-template/workflows/pipeline.nf

@@ -23,8 +23,9 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+ch_multiqc_config                     = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+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)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -89,10 +90,14 @@ workflow {{ short_name|upper }} {
     workflow_summary    = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params)
     ch_workflow_summary = Channel.value(workflow_summary)
 
+    methods_description    = WorkflowTestpipeline.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+    ch_methods_description = Channel.value(methods_description)
+
     ch_multiqc_files = Channel.empty()
     ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
     ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))