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make fastp output optional
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peterpru committed Nov 15, 2024
1 parent a30ab4b commit 8a72c28
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion workflows/raredisease.nf
Original file line number Diff line number Diff line change
Expand Up @@ -902,7 +902,7 @@ 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(FASTP.out.json.collect{it[1]}.ifEmpty{null}).filter {it!=null}
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([]))
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