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add ngsbits output
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peterpru authored Nov 11, 2024
1 parent 3d598b7 commit ef2f644
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion workflows/raredisease.nf
Original file line number Diff line number Diff line change
Expand Up @@ -902,12 +902,13 @@ workflow RAREDISEASE {
)

ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]}.ifEmpty([])))
ch_multiqc_files = ch_multiqc_files.mix(NGSBITS_SAMPLEGENDER.out.tsv.collect{it[1]}.ifEmpty([])))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]}.ifEmpty([])))


if (!params.skip_peddy) {
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