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Add long read preprocessing subworkflow

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ljmesi 2022-03-18 15:10:44 +01:00
parent 16be676d72
commit 1e42f1d9f2
1 changed files with 34 additions and 0 deletions
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subworkflows/local/longread_preprocessing.nf Normal file
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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
workflow LONGREAD_PREPROCESSING {
take:
reads
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads
.dump(tag: "pre_fastqc_check")
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
FASTQC_POST ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}