.map { patient_sample, ch_items -> // get number of lanes per sample [ patient_sample, ch_items.size() ] } .combine(ch_with_patient_sample, by: 0) // for each entry add numLanes .map { patient_sample, num_lanes, ch_items -> (meta, fastq_1, fastq_2, table, cram, crai,...
"--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" } } withName: 'MERGE_MUTECT2.*' { ext.prefix = { "${meta.id}.mutect2" } publishDir = [ ext.prefix = { "${meta.id}.mutect2" } publishDir = [ mode: params.publish_...