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37 lines
1.2 KiB
Text
37 lines
1.2 KiB
Text
/*
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Process long raw reads with porechop
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*/
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
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include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
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workflow LONGREAD_PREPROCESSING {
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take:
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reads
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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PORECHOP ( reads )
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ch_processed_reads = PORECHOP.out.reads
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.dump(tag: "pre_fastqc_check")
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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'] = 1
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[ meta_new, reads ]
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}
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FASTQC_PROCESSED ( PORECHOP.out.reads )
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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