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Code Issues Releases Packages Activity

Simplify params which control host removal publish

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This commit is contained in:
ljmesi 2022-05-05 09:07:33 +02:00
parent 5b7b214156
commit d94534e8ac
3 changed files with 5 additions and 25 deletions
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8
conf/modules.config
View file

@ -169,7 +169,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/minimap2/index" }, path: { "${params.outdir}/minimap2/index" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_minimap2_hostremoval_index, enabled: params.save_hostremoval_index,
pattern: 'minimap2' pattern: 'minimap2'
] ]
} }
@ -179,7 +179,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/minimap2/align" }, path: { "${params.outdir}/minimap2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_minimap2_hostremoval_mapped, enabled: params.save_hostremoval_mapped,
pattern: '*.bam' pattern: '*.bam'
] ]
} }
@ -190,7 +190,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/samtools/view" }, path: { "${params.outdir}/samtools/view" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_samtools_unmapped_bam, enabled: params.save_hostremoval_unmapped,
pattern: '*.bam' pattern: '*.bam'
] ]
} }
@ -200,7 +200,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/samtools/bam2fq" }, path: { "${params.outdir}/samtools/bam2fq" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_minimap2_unmapped_fq, enabled: params.save_hostremoval_unmapped,
pattern: '*.fq.gz' pattern: '*.fq.gz'
] ]
} }

6
nextflow.config
View file

@ -84,14 +84,10 @@ 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
longread_hostremoval_index = null
save_hostremoval_index = false save_hostremoval_index = false
save_hostremoval_mapped = false save_hostremoval_mapped = false
save_hostremoval_unmapped = false save_hostremoval_unmapped = false
longread_hostremoval_index = null
save_minimap2_hostremoval_index = false
save_minimap2_hostremoval_mapped = false
save_samtools_unmapped_bam = false
save_minimap2_unmapped_fq = false
// MALT // MALT

16
nextflow_schema.json
View file

@ -401,22 +401,6 @@
"longread_hostremoval_index": { "longread_hostremoval_index": {
"type": "string", "type": "string",
"default": "None" "default": "None"
},
"save_minimap2_hostremoval_index": {
"type": "boolean",
"description": "Flag for publishing minimap2 host removal index"
},
"save_minimap2_hostremoval_mapped": {
"type": "boolean",
"description": "Flag for publishinig bam file with all long reads mapped to a reference"
},
"save_samtools_unmapped_bam": {
"type": "boolean",
"description": "Flag for publishing bam for reads that did not map to the host reference"
},
"save_minimap2_unmapped_fq": {
"type": "boolean",
"description": "Flag for publishing fastq files for reads that did not map to the host reference"
} }
} }
} }