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Fix publishing of log files of rpreprocessing steps

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This commit is contained in:
James Fellows Yates 2022-12-15 10:35:06 +01:00
parent 578081df2e
commit 88589fbc53
1 changed files with 100 additions and 44 deletions
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144
conf/modules.config
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@ -61,10 +61,17 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/fastp" },
pattern: '*.fastq.gz', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
] ]
} }
@ -82,10 +89,17 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/fastp" },
pattern: '*.fastq.gz', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
] ]
} }
@ -98,10 +112,17 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/adapterremoval" },
pattern: '*.fastq.gz', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
] ]
} }
@ -117,20 +138,34 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/adapterremoval" },
pattern: '*.fastq.gz', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
] ]
} }
withName: PORECHOP_PORECHOP { withName: PORECHOP_PORECHOP {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/porechop" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/porechop" },
pattern: '*.fastq.gz', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
] ]
} }
@ -143,10 +178,17 @@ process {
.join(' ').trim() .join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" } ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
publishDir = [ publishDir = [
path: { "${params.outdir}/filtlong" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/filtlong" },
pattern: '*.{fastq.gz,log}', mode: params.publish_dir_mode,
enabled: params.save_preprocessed_reads pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
],
[
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
] ]
} }
@ -163,21 +205,21 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.log' pattern: '*.log'
], ],
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped, enabled: params.save_hostremoval_mapped,
pattern: '*.bam' pattern: '*.bam'
], ],
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped, enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
] ]
} }
@ -240,10 +282,17 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/bbduk/" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/bbduk/" },
pattern: '*.{fastq.gz,log}', mode: params.publish_dir_mode,
enabled: params.save_complexityfiltered_reads pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
] ]
} }
@ -255,10 +304,17 @@ process {
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/prinseqplusplus/" }, [
mode: params.publish_dir_mode, path: { "${params.outdir}/prinseqplusplus/" },
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}', mode: params.publish_dir_mode,
enabled: params.save_complexityfiltered_reads pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
] ]
} }
@ -318,7 +374,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/bracken/" }, path: { "${params.outdir}/bracken/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.{txt}' pattern: '*.txt'
] ]
} }