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Added possibility of specifying kit for split-pipe #45

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Merged
bonitavw merged 1 commit into from
Feb 6, 2026
Merged

Added possibility of specifying kit for split-pipe #45

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6 changes: 5 additions & 1 deletion modules/local/pipelines/split-pipe/split-pipe_demux/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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}"
Expand All @@ -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}
"""
}
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