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Some more cleanup

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This commit is contained in:
James Fellows Yates 2022-03-25 15:22:41 +01:00
parent b5f5c75504
commit 7ddcb09a85
1 changed files with 64 additions and 0 deletions
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subworkflows/local/shortread_adapterremoval.nf Normal file
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/*
Process raw reads with AdapterRemoval
*/
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
workflow SHORTREAD_FASTP {
take:
reads // file: /path/to/samplesheet.csv
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// STEP: Read clipping and merging
//
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
ch_input_for_fastp = reads
.dump(tag: "pre-fastp_branch")
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
}
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
if ( params.shortread_clipmerge_mergepairs ) {
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
.mix( FASTP_SINGLE.out.reads )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
} else {
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
.mix( FASTP_SINGLE.out.reads )
}
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
ch_processed_reads = ch_fastp_reads_prepped.dump(tag: "ch_fastp_reads_prepped")
ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
ch_multiqc_files.dump(tag: "preprocessing_fastp_mqc_final")
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}