Merge pull request #145 from Aratz/fix_multiqc_report

Fix MultiQC report generation
nf-core · Oct 17, 2023 · 3df96fc · 3df96fc
2 parents 3340915 + 9236c6f
commit 3df96fc
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#127](https://github.com/nf-core/demultiplex/pull/127) Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0
 - [#140](https://github.com/nf-core/demultiplex/pull/140) Make it possible to skip MultiQC, fix error raising
+- [#145](https://github.com/nf-core/demultiplex/pull/145) Fix MultiQC report generation
 
 ## `Removed`
 

diff --git a/tests/pipeline/bclconvert.nf.test b/tests/pipeline/bclconvert.nf.test
@@ -20,10 +20,10 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert workflow.trace.succeeded().size() == 6 },
-                // FIXME https://github.com/nf-core/demultiplex/issues/64
-                // { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bylane.txt"),
-                //                 path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"),
-                //                 path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bysample.txt")).match("multiqc") },
+                { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bylane.txt"),
+                        path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"),
+                        path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bysample.txt")
+                    ).match("multiqc") },
                 { assert snapshot(path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_summary.txt"),

diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
@@ -228,7 +228,6 @@ workflow DEMULTIPLEX {
         methods_description    = WorkflowDemultiplex.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
         ch_methods_description = Channel.value(methods_description)
 
-        ch_multiqc_files = Channel.empty()
         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())