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Rename shortread subworkflow to be more consistent

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ljmesi 2022-03-21 18:25:56 +01:00
parent c97de32434
commit f6fe26de46
2 changed files with 4 additions and 4 deletions
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0
subworkflows/local/preprocessing.nf → subworkflows/local/shortread_preprocessing.nf
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8
workflows/taxprofiler.nf
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@ -39,7 +39,7 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
include { INPUT_CHECK } from '../subworkflows/local/input_check' include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check' include { DB_CHECK } from '../subworkflows/local/db_check'
include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing' include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing' include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
/* /*
@ -101,7 +101,7 @@ workflow TAXPROFILER {
// PERFORM PREPROCESSING // PERFORM PREPROCESSING
// //
if ( params.fastp_clip_merge ) { if ( params.fastp_clip_merge ) {
FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq ) SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
} }
ch_multiqc_files = Channel.empty() ch_multiqc_files = Channel.empty()
@ -118,7 +118,7 @@ workflow TAXPROFILER {
// //
// PERFORM RUN MERGING // PERFORM RUN MERGING
// //
ch_processed_for_combine = FASTQ_PREPROCESSING.out.reads ch_processed_for_combine = SHORTREAD_PREPROCESSING.out.reads
.dump(tag: "prep_for_combine_grouping") .dump(tag: "prep_for_combine_grouping")
.map { .map {
meta, reads -> meta, reads ->
@ -203,7 +203,7 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.fastp_clip_merge) { if (params.fastp_clip_merge) {
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc) ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
} }
if (params.run_kraken2) { if (params.run_kraken2) {
ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))