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

7
nextflow.config
View file

@ -82,8 +82,11 @@ params {
// Host Removal
perform_shortread_hostremoval = false
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_mapped = false
save_hostremoval_unmapped = false
// MALT
run_malt = false

39
nextflow_schema.json
View file

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