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docs/output.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline.
+This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 

docs/usage.md

@@ -93,7 +93,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you
 
 First, go to the [nf-core/bamtofastq releases page](https://github.com/nf-core/bamtofastq/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 

main.nf

@@ -50,6 +50,8 @@ workflow NFCORE_BAMTOFASTQ {
     BAMTOFASTQ (
         samplesheet
     )
+    emit:
+    multiqc_report = BAMTOFASTQ.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -87,7 +89,8 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url
+        params.hook_url,
+        NFCORE_BAMTOFASTQ.out.multiqc_report
     )
 }
 

subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf

@@ -105,7 +105,7 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
-
+    multiqc_report // string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
@@ -122,7 +122,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                []
+                multiqc_report.toList()
             )
         }
 
@@ -186,8 +186,8 @@ def toolCitationText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
-
-
+            "FastQC (Andrews 2010),",
+            "MultiQC (Ewels et al. 2016)",
             "."
         ].join(' ').trim()
 
@@ -199,8 +199,8 @@ 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 = [
-
-
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            "<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>"
         ].join(' ').trim()
 
     return reference_text

tower.yml

@@ -1,3 +1,5 @@
 reports:
+  multiqc_report.html:
+    display: "MultiQC HTML report"
   samplesheet.csv:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"

workflows/bamtofastq.nf

@@ -4,8 +4,8 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_bamtofastq_pipeline'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 
@@ -184,7 +184,7 @@ workflow BAMTOFASTQ {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  + 'pipeline_software_' +  ''  + 'versions.yml',
+            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }