diff --git a/CHANGELOG.md b/CHANGELOG.md index 0c39bd12..2c664482 100755 --- 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 index c9dc7a21..2b56f27c 100644 --- 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 index 3ddcb32f..4f37ee2e 100644 --- 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())