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https://github.com/MillironX/taxprofiler.git
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Rename subworkflow parameters for consistency
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parent
16a3556bfc
commit
dfeaa0d1fe
6 changed files with 35 additions and 34 deletions
8
.github/workflows/ci.yml
vendored
8
.github/workflows/ci.yml
vendored
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@ -29,8 +29,8 @@ jobs:
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- NXF_VER: ""
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NXF_EDGE: "1"
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parameters:
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- "--longread_clip false"
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- "--shortread_clip false"
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- "--perform_longread_clip false"
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- "--perform_shortread_clipmerge false"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
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@ -39,8 +39,8 @@ jobs:
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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- "--run_merging"
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- "--run_merging --shortread_clipmerge_mergepairs"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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steps:
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- name: Check out pipeline code
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@ -173,7 +173,7 @@ process {
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -183,7 +183,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -193,7 +193,7 @@ process {
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -28,7 +28,7 @@ params {
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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shortread_clipmerge = true
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longread_clip = false
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shortread_complexityfilter = true
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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}
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@ -55,7 +55,7 @@ params {
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databases = null
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// FASTQ preprocessing
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shortread_clipmerge = false
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perform_shortread_clipmerge = false
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shortread_clipmerge_tool = 'fastp'
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shortread_clipmerge_skipadaptertrim = false
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shortread_clipmerge_mergepairs = false
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@ -63,11 +63,11 @@ params {
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shortread_clipmerge_adapter1 = null
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_minlength = 15
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longread_clip = false
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perform_longread_clip = false
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save_preprocessed_reads = false
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// Complexity filtering
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shortread_complexityfilter = false
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perform_shortread_complexityfilter = false
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shortread_complexityfilter_tool = 'bbduk'
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shortread_complexityfilter_entropy = 0.3
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shortread_complexityfilter_bbduk_windowsize = 50
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@ -77,7 +77,7 @@ params {
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save_complexityfiltered_reads = false
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// run merging
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run_merging = false
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perform_runmerging = false
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save_runmerged_reads = false
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// MALT
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@ -92,6 +92,7 @@ params {
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centrifuge_save_unaligned = false
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centrifuge_save_aligned = false
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centrifuge_sam_format = false
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// metaphlan3
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run_metaphlan3 = false
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}
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@ -262,15 +262,9 @@
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"type": "string",
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"default": "None"
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},
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"shortread_clipmerge": {
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"type": "boolean"
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},
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"shortread_clipmerge_excludeunmerged": {
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"type": "boolean"
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},
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"longread_clip": {
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"type": "boolean"
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},
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"run_malt": {
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"type": "boolean"
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},
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@ -334,9 +328,6 @@
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"shortread_complexityfilter_bbduk_mask": {
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"type": "boolean"
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},
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"shortread_complexityfilter": {
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"type": "boolean"
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},
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"shortread_complexityfilter_entropy": {
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"type": "number",
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"default": 0.3
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@ -353,10 +344,19 @@
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"save_complexityfiltered_reads": {
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"type": "boolean"
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},
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"run_merging": {
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"save_runmerged_reads": {
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"type": "boolean"
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},
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"save_runmerged_reads": {
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"perform_shortread_clipmerge": {
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"type": "boolean"
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},
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"perform_longread_clip": {
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"type": "boolean"
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},
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"perform_shortread_complexityfilter": {
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"type": "boolean"
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},
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"perform_runmerging": {
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"type": "boolean"
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}
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}
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@ -101,14 +101,14 @@ workflow TAXPROFILER {
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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.shortread_clipmerge ) {
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if ( params.perform_shortread_clipmerge ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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}
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if ( params.longread_clip ) {
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if ( params.perform_longread_clip ) {
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ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
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.map { it -> [ it[0], [it[1]] ] }
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} else {
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@ -119,7 +119,7 @@ workflow TAXPROFILER {
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SUBWORKFLOW: COMPLEXITY FILTERING
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*/
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if ( params.shortread_complexityfilter ) {
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if ( params.perform_shortread_complexityfilter ) {
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ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
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} else {
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ch_shortreads_filtered = ch_shortreads_preprocessed
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@ -129,7 +129,7 @@ workflow TAXPROFILER {
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STEP: Run merging
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*/
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if ( params.run_merging ) {
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if ( params.perform_runmerging ) {
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ch_reads_for_cat_branch = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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@ -190,22 +190,22 @@ 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.shortread_clipmerge) {
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if (params.perform_shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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}
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if (params.longread_clip) {
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if (params.perform_longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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}
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if (params.shortread_complexityfilter){
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if (params.perform_shortread_complexityfilter){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.run_merging){
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if (params.perform_runmerging){
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ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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}
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