Add rename in the MultiQC report for samples without techreps

CHANGELOG.md

@@ -100,6 +100,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules
 - [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs
 - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
+- [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add wholesale rename in the MultiQC report
 
 ### Parameters
 

modules.json

@@ -92,7 +92,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "45d482f013f7da8a3e050e855f04ada418d91c3c",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {

workflows/rnaseq/assets/multiqc/multiqc_config.yml

@@ -10,6 +10,7 @@ report_section_order:
 
 export_plots: true
 disable_version_detection: true
+sample_names_replace_exact: true
 
 # Run only these modules
 run_modules:

workflows/rnaseq/main.nf

@@ -857,6 +857,7 @@ workflow RNASEQ {
     // MODULE: MultiQC
     //
     ch_multiqc_report = Channel.empty()
+
     if (!params.skip_multiqc) {
         ch_multiqc_config        = Channel.fromPath("$projectDir/workflows/rnaseq/assets/multiqc/multiqc_config.yml", checkIfExists: true)
         ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
@@ -866,11 +867,29 @@ workflow RNASEQ {
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
 
+        // Provide MultiQC with rename patterns to ensure it uses sample names
+        // for single-techrep samples not processed by CAT_FASTQ.
+
+        ch_name_replacements = ch_fastq.single
+            .map{ meta, reads ->
+                def name1 = file(reads[0]).simpleName + "\t" + meta.id + '_1'
+                if (reads[1] ){
+                    def name2 = file(reads[1]).simpleName + "\t" + meta.id + '_2'
+                    return [ name1, name2 ]
+                } else{
+                    return name1
+                }
+            }
+            .flatten()
+            .collectFile(name: 'name_replacement.txt', newLine: true)
+
         MULTIQC (
             ch_multiqc_files.collect(),
             ch_multiqc_config.toList(),
             ch_multiqc_custom_config.toList(),
-            ch_multiqc_logo.toList()
+            ch_multiqc_logo.toList(),
+            ch_name_replacements,
+            []
         )
         ch_multiqc_report = MULTIQC.out.report
     }