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refactor: use flags to publish reads

This commit is contained in:
Moritz E. Beber 2022-04-06 10:27:11 +02:00
parent 018b9a8ea6
commit 7ab3aa546b
3 changed files with 24 additions and 11 deletions

View file

@ -28,10 +28,6 @@ process {
] ]
} }
withName: UNTAR {
publishDir = [enabled: false]
}
withName: FASTQC { withName: FASTQC {
ext.args = '--quiet' ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" } ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
@ -64,7 +60,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
] ]
} }
@ -83,7 +80,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
] ]
} }
@ -99,7 +97,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
] ]
} }
@ -118,7 +117,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
] ]
} }
@ -127,7 +127,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/porechop" }, path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
] ]
} }
@ -141,7 +142,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/bbduk/" }, path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}' pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
] ]
} }
@ -154,7 +156,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/prinseqplusplus/" }, path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}' pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
] ]
} }

View file

@ -64,6 +64,7 @@ params {
shortread_clipmerge_adapter2 = null shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15 shortread_clipmerge_minlength = 15
longread_clip = false longread_clip = false
save_preprocessed_reads = false
// Complexity filtering // Complexity filtering
shortread_complexityfilter = false shortread_complexityfilter = false
@ -73,6 +74,7 @@ params {
shortread_complexityfilter_bbduk_mask = false shortread_complexityfilter_bbduk_mask = false
shortread_complexityfilter_prinseqplusplus_mode = 'entropy' shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5 shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false
// MALT // MALT

View file

@ -308,6 +308,10 @@
"type": "integer", "type": "integer",
"default": 15 "default": 15
}, },
"save_preprocessed_reads": {
"type": "boolean",
"default": false
},
"shortread_complexityfilter_tool": { "shortread_complexityfilter_tool": {
"type": "string", "type": "string",
"default": "bbduk" "default": "bbduk"
@ -334,6 +338,10 @@
"shortread_complexityfilter_prinseqplusplus_dustscore": { "shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number", "type": "number",
"default": 0.5 "default": 0.5
},
"save_complexityfiltered_reads": {
"type": "boolean",
"default": false
} }
} }
} }