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Rename shortread subworkflow to be more consistent
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parent
c97de32434
commit
f6fe26de46
2 changed files with 4 additions and 4 deletions
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@ -39,7 +39,7 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
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include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { DB_CHECK } from '../subworkflows/local/db_check'
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include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
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include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
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include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
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/*
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@ -101,7 +101,7 @@ workflow TAXPROFILER {
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// PERFORM PREPROCESSING
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//
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if ( params.fastp_clip_merge ) {
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FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
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SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
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}
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ch_multiqc_files = Channel.empty()
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@ -118,7 +118,7 @@ workflow TAXPROFILER {
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//
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// PERFORM RUN MERGING
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//
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ch_processed_for_combine = FASTQ_PREPROCESSING.out.reads
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ch_processed_for_combine = SHORTREAD_PREPROCESSING.out.reads
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.dump(tag: "prep_for_combine_grouping")
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.map {
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meta, reads ->
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@ -203,7 +203,7 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.fastp_clip_merge) {
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ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
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}
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if (params.run_kraken2) {
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ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))
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