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Code Issues Releases Packages Activity

Add finer controler over for hostremoval saving

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This commit is contained in:
James Fellows Yates 2022-04-17 22:27:04 +02:00
parent fc8a83245a
commit 2cfcdf2dd2
3 changed files with 53 additions and 13 deletions
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20
conf/modules.config
View file

@ -133,21 +133,33 @@ process {
} }
withName: BOWTIE2_BUILD { withName: BOWTIE2_BUILD {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/bowtie2/build" }, path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.bt2' enabled: params.save_hostremoval_index,
pattern: 'bowtie2/*'
] ]
} }
withName: BOWTIE2_ALIGN { withName: BOWTIE2_ALIGN {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped,
pattern: '*.bam'
],
publishDir = [ publishDir = [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,bam}' enabled: params.save_hostremoval_unmapped,
] pattern: '*.fastq.gz'
]]
} }
withName: BBMAP_BBDUK { withName: BBMAP_BBDUK {

3
nextflow.config
View file

@ -84,6 +84,9 @@ params {
perform_shortread_hostremoval = false perform_shortread_hostremoval = false
shortread_hostremoval_reference = null shortread_hostremoval_reference = null
shortread_hostremoval_index = null shortread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_mapped = false
save_hostremoval_unmapped = false
// MALT // MALT
run_malt = false run_malt = false

37
nextflow_schema.json
View file

@ -10,7 +10,10 @@
"type": "object", "type": "object",
"fa_icon": "fas fa-terminal", "fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.", "description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"], "required": [
"input",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -173,7 +176,14 @@
"description": "Method used to save pipeline results to output directory.", "description": "Method used to save pipeline results to output directory.",
"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.", "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.",
"fa_icon": "fas fa-copy", "fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true "hidden": true
}, },
"email_on_fail": { "email_on_fail": {
@ -294,7 +304,10 @@
"shortread_clipmerge_tool": { "shortread_clipmerge_tool": {
"type": "string", "type": "string",
"default": "fastp", "default": "fastp",
"enum": ["fastp", "adapterremoval"] "enum": [
"fastp",
"adapterremoval"
]
}, },
"shortread_clipmerge_skipadaptertrim": { "shortread_clipmerge_skipadaptertrim": {
"type": "boolean" "type": "boolean"
@ -335,7 +348,10 @@
"shortread_complexityfilter_prinseqplusplus_mode": { "shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string", "type": "string",
"default": "entropy", "default": "entropy",
"enum": ["entropy", "dust"] "enum": [
"entropy",
"dust"
]
}, },
"shortread_complexityfilter_prinseqplusplus_dustscore": { "shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number", "type": "number",
@ -364,11 +380,20 @@
}, },
"shortread_hostremoval_reference": { "shortread_hostremoval_reference": {
"type": "string", "type": "string",
"default": null "default": "None"
}, },
"shortread_hostremoval_index": { "shortread_hostremoval_index": {
"type": "string", "type": "string",
"default": null "default": "None"
},
"save_hostremoval_index": {
"type": "boolean"
},
"save_hostremoval_mapped": {
"type": "boolean"
},
"save_hostremoval_unmapped": {
"type": "boolean"
} }
} }
} }