From 8a72c28bb775cdb33208d1e9026be9cfc7d5882d Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 15 Nov 2024 12:03:02 +0100 Subject: [PATCH] make fastp output optional --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 6c9ba228..8ba77f94 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -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([]))