diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index 0631ba67..cc22534d 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -270,7 +270,7 @@ workflow DEMULTIPLEX { // Prepare metamap with fastq info ch_meta_fastq = ch_raw_fastq.map { meta, fastq_files -> // Determine the publish directory based on the lane information - meta.publish_dir = publish_dir = meta.lane ? "${params.outdir}/${meta.fcid}/L00${meta.lane}" : "${params.outdir}/${meta.fcid}" //Must be fcid because id gets modified + meta.publish_dir = meta.lane ? "${params.outdir}/${meta.fcid}/L00${meta.lane}" : "${params.outdir}/${meta.fcid}" //Must be fcid because id gets modified meta.fastq_1 = "${meta.publish_dir}/${fastq_files[0].getName()}" // Add full path for fastq_2 to the metadata if the sample is not single-end