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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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parent
0d0b377dfb
commit
14f2b7bd84
2 changed files with 10 additions and 12 deletions
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@ -17,14 +17,16 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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ch_input_for_adapterremoval = reads
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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single: it[0].single_end
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paired: !it[0].single_end
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}
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ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, [] )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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// due to the slightly ugly output implementation of the current AdapterRemoval2 module, each file
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// has to be exported in a separate channel, and we must manually recombine when necessary
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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@ -35,16 +37,14 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = true
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meta_new.single_end = true
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[ meta_new, reads ]
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}
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.groupTuple(by: 0)
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.groupTuple()
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ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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@ -58,9 +58,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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}
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.groupTuple(by: 0)
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ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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} else {
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@ -21,8 +21,8 @@ workflow SHORTREAD_PREPROCESSING {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
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} else if ( params.shortread_clipmerge_tool == "adapterremoval" ) {
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ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads
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ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
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ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
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} else {
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ch_processed_reads = reads
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}
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