diff --git a/modules/local/pipelines/split-pipe/split-pipe_demux/main.nf b/modules/local/pipelines/split-pipe/split-pipe_demux/main.nf index 0520908..e46b1be 100644 --- a/modules/local/pipelines/split-pipe/split-pipe_demux/main.nf +++ b/modules/local/pipelines/split-pipe/split-pipe_demux/main.nf @@ -13,6 +13,9 @@ process PARSEBIO_PIPELINE_DEMUX { tuple val(meta), path("*group*_R1*"), path("*group*_R2*"), path(fastq_indices), path(input_file), emit: splitted_files script: + // Retrieve kit specification for split-pipe from custom parameters if set, otherwise from conf/seqtech_parameters.config + def kit_specification = params.splitpipe_kit ? "--kit ${params.splitpipe_kit} --kit_score_skip" : '' + """ echo "\n\n================== split-pipe Demultiplex ==================" echo "split-pipe script: ${params.splitpipe_demultiplex_script}" @@ -28,6 +31,7 @@ process PARSEBIO_PIPELINE_DEMUX { --fq1 ${fastq_cDNA} \\ --fq2 ${fastq_BC_UMI} \\ --opath . \\ - --group ${meta.id} ${meta.rt} + --group ${meta.id} ${meta.rt} \\ + ${kit_specification} """ }