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refactor: use flags to publish reads
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parent
018b9a8ea6
commit
7ab3aa546b
3 changed files with 24 additions and 11 deletions
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@ -28,10 +28,6 @@ process {
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]
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}
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withName: UNTAR {
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publishDir = [enabled: false]
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}
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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@ -64,7 +60,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -83,7 +80,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -99,7 +97,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -118,7 +117,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -127,7 +127,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -141,7 +142,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}'
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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}
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@ -154,7 +156,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}'
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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}
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@ -64,6 +64,7 @@ params {
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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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save_preprocessed_reads = false
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// Complexity filtering
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shortread_complexityfilter = false
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@ -73,6 +74,7 @@ params {
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shortread_complexityfilter_bbduk_mask = false
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shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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save_complexityfiltered_reads = false
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// MALT
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@ -308,6 +308,10 @@
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"type": "integer",
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"default": 15
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},
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"save_preprocessed_reads": {
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"type": "boolean",
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"default": false
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},
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk"
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@ -334,6 +338,10 @@
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"default": 0.5
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},
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"save_complexityfiltered_reads": {
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"type": "boolean",
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"default": false
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}
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}
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}
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