mirror of
https://github.com/MillironX/taxprofiler.git
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Add final adapterremoval options to match fastp functionality
This commit is contained in:
James Fellows Yates
parent
c4c93bd59d
commit
dcda815bfb
4 changed files with 71 additions and 34 deletions
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@ -62,18 +62,15 @@ process {
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]
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}
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withName: FASTP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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withName: FASTP_SINGLE {
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ext.args = [
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// collapsing options - option to retain singletons
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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@ -81,6 +78,61 @@ process {
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]
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}
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withName: FASTP_PAIRED {
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ext.args = [
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// collapsing options - option to retain singletons
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: ADAPTERREMOVAL_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
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// filtering options
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"--minlength ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: ADAPTERREMOVAL_PAIRED {
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ext.args = [
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// collapsing options
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params.shortread_clipmerge_mergepairs ? "--collapse" : "",
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// trimming options
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params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
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params.shortread_clipmerge_adapter2 ? "--adapter2 ${params.shortread_clipmerge_adapter2}" : "",
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// filtering options
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"--minlength ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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@ -99,23 +151,23 @@ process {
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${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: 'copy',
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${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: 'copy',
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pattern: '*.{fastq.gz,txt}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -59,7 +59,7 @@ params {
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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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shortread_clipmerge_excludeunmerged = true
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shortread_clipmerge_excludeunmerged = false
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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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@ -10,10 +10,7 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": [
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"input",
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"outdir"
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],
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"required": ["input", "outdir"],
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"properties": {
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"input": {
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"type": "string",
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@ -176,14 +173,7 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"hidden": true
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},
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"email_on_fail": {
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@ -277,7 +267,7 @@
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},
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"shortread_clipmerge_excludeunmerged": {
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"type": "boolean",
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"default": true
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"default": false
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},
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"longread_clip": {
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"type": "boolean"
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@ -295,10 +285,7 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": [
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"fastp",
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"adapterremoval"
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]
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"enum": ["fastp", "adapterremoval"]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -319,4 +306,4 @@
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"default": 15
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}
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}
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}
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}
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@ -16,7 +16,6 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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ch_multiqc_files = Channel.empty()
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ch_input_for_adapterremoval = reads
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.dump(tag: "pre_adapterremoval_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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@ -36,11 +35,13 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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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['single_end'] = true
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[ meta_new, reads ]
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}
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.groupTuple(by: 0)
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ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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@ -51,7 +52,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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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['single_end'] = true
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[ meta_new, reads ]
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}
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@ -65,13 +66,10 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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ch_adapterremoval_reads_prepped_pe = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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.join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
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.dump(tag: "pre-group")
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.groupTuple(by: 0)
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.dump(tag: "post-group")
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.map { meta, pair1, pair2 ->
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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.dump(tag: "post-map")
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe
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