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Merge pull request #43 from nf-core/refactor-config

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Refactor config
This commit is contained in:
James A. Fellows Yates 2022-04-06 11:03:45 +02:00 committed by GitHub
commit 4c4475c316
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 33 additions and 30 deletions
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53
conf/modules.config
View file

@ -12,12 +12,6 @@
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
@ -34,20 +28,12 @@ process {
]
}
withName: UNTAR {
publishDir = [
path: { "${params.outdir}/databases" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: FASTQC {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
publishDir = [
path: { "${params.outdir}/fastqc/raw" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.html'
]
}
@ -57,7 +43,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [
path: { "${params.outdir}/fastqc/processed" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.html'
]
}
@ -73,8 +59,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -92,8 +79,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/fastp" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -108,8 +96,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -127,8 +116,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/adapterremoval" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -136,8 +126,9 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/porechop" },
mode: 'copy',
pattern: '*.fastq.gz'
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
@ -151,7 +142,8 @@ process {
publishDir = [
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}'
pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
]
}
@ -164,7 +156,8 @@ process {
publishDir = [
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}'
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
]
}
@ -173,7 +166,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.{rma6,tab,text,sam,log}'
]
}
@ -183,7 +176,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,txt}'
]
}

2
nextflow.config
View file

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

8
nextflow_schema.json
View file

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