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Add finer controler over for hostremoval saving
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parent
fc8a83245a
commit
2cfcdf2dd2
3 changed files with 53 additions and 13 deletions
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@ -133,21 +133,33 @@ process {
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}
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withName: BOWTIE2_BUILD {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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pattern: '*.bt2'
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2/*'
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]
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}
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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],
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publishDir = [
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,bam}'
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]
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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]]
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}
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withName: BBMAP_BBDUK {
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@ -84,6 +84,9 @@ params {
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perform_shortread_hostremoval = false
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shortread_hostremoval_reference = null
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shortread_hostremoval_index = null
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save_hostremoval_index = false
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save_hostremoval_mapped = false
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save_hostremoval_unmapped = false
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// MALT
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run_malt = false
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@ -10,7 +10,10 @@
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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": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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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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"hidden": true
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},
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"email_on_fail": {
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@ -294,7 +304,10 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -335,7 +348,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -364,11 +380,20 @@
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},
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"shortread_hostremoval_reference": {
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"type": "string",
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"default": null
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"default": "None"
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},
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"shortread_hostremoval_index": {
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"type": "string",
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"default": null
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"default": "None"
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},
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"save_hostremoval_index": {
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"type": "boolean"
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},
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"save_hostremoval_mapped": {
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"type": "boolean"
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},
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"save_hostremoval_unmapped": {
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"type": "boolean"
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}
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}
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}
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