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Fix file header descriptions
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commit
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2 changed files with 9 additions and 10 deletions
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@ -1,6 +1,9 @@
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/*
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Process long raw reads with porechop
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*/
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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
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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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include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
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workflow LONGREAD_PREPROCESSING {
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workflow LONGREAD_PREPROCESSING {
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take:
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take:
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@ -23,7 +26,7 @@ workflow LONGREAD_PREPROCESSING {
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FASTQC_POST ( PORECHOP.out.reads )
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FASTQC_POST ( PORECHOP.out.reads )
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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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_POST.out.zip.collect{it[1]} )
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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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emit:
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@ -1,7 +1,6 @@
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//
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/*
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// Check input samplesheet and get read channels
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Process short raw reads with FastP
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//
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*/
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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@ -17,9 +16,6 @@ workflow SHORTREAD_FASTP {
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//
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//
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// STEP: Read clipping and merging
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// STEP: Read clipping and merging
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//
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//
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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ch_input_for_fastp = reads
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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.dump(tag: "pre-fastp_branch")
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.branch{
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.branch{
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