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This commit is contained in:
Sofia Stamouli 2022-10-24 16:28:07 +02:00
parent 19231538da
commit d3d4297ca9
1 changed files with 4 additions and 4 deletions
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workflows/taxprofiler.nf
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@ -257,12 +257,12 @@ workflow TAXPROFILER {
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())
if (!params.preprocessing_qc_tool == 'falco') {
if ( params.preprocessing_qc_tool == 'falco' ) {
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
} else {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
}
else {
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
}
if (params.perform_shortread_qc) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )