diff --git a/software/multiqc/main.nf b/software/multiqc/main.nf index 80dfb0c5..09d223fc 100644 --- a/software/multiqc/main.nf +++ b/software/multiqc/main.nf @@ -24,9 +24,8 @@ process MULTIQC { script: def software = getSoftwareName(task.process) - def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : '' """ - multiqc -f $options.args $custom_config . - multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt + multiqc -f $options.args . + multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt """ } diff --git a/software/multiqc/meta.yml b/software/multiqc/meta.yml index 4fac4394..684ccd5e 100644 --- a/software/multiqc/meta.yml +++ b/software/multiqc/meta.yml @@ -33,14 +33,18 @@ input: description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC output: - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - report: type: file description: MultiQC report file pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" - version: type: file description: File containing software version @@ -48,3 +52,4 @@ output: authors: - "@abhi18av" - "@bunop" + - "@drpatelh" diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf index ab25e8c3..06b466ab 100644 --- a/tests/software/multiqc/main.nf +++ b/tests/software/multiqc/main.nf @@ -5,14 +5,11 @@ nextflow.enable.dsl = 2 include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc']) include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end']) -ch_multiqc_config = file("$launchDir/tests/software/multiqc/multiqc_config.yml", checkIfExists: true) - workflow test_multiqc { test_paired_end() input = [ - ch_multiqc_config - .mix(test_paired_end.out.zip.collect { it[1] }.ifEmpty([])) + test_paired_end.out.zip.collect { it[1] }.ifEmpty([]) ] MULTIQC(*input) diff --git a/tests/software/multiqc/multiqc_config.yml b/tests/software/multiqc/multiqc_config.yml deleted file mode 100644 index e69de29b..00000000