mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 17:09:54 +00:00
Merge pull request #192 from nf-core/publishing-fix
Fix publishing of log files of rpreprocessing steps
This commit is contained in:
James A. Fellows Yates
GitHub
commit
aa117e8af9
4 changed files with 125 additions and 50 deletions
|
|
@ -33,7 +33,7 @@ process {
|
|||
}
|
||||
|
||||
withName: FALCO {
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/falco/raw" },
|
||||
mode: params.publish_dir_mode,
|
||||
|
|
@ -42,7 +42,7 @@ process {
|
|||
}
|
||||
|
||||
withName: FALCO_PROCESSED {
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/falco/processed" },
|
||||
mode: params.publish_dir_mode,
|
||||
|
|
@ -61,10 +61,17 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{log,html,json}'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -82,10 +89,17 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/fastp" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{log,html,json}'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -98,10 +112,17 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.settings'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -117,20 +138,34 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/adapterremoval" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.settings'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
withName: PORECHOP_PORECHOP {
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/porechop" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/porechop" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/porechop" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -143,10 +178,17 @@ process {
|
|||
.join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/filtlong" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{fastq.gz,log}',
|
||||
enabled: params.save_preprocessed_reads
|
||||
[
|
||||
path: { "${params.outdir}/filtlong" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.fastq.gz',
|
||||
enabled: params.save_preprocessed_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/filtlong" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -163,21 +205,21 @@ process {
|
|||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
[
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_mapped,
|
||||
pattern: '*.bam'
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_mapped,
|
||||
pattern: '*.bam'
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_unmapped,
|
||||
pattern: '*.fastq.gz'
|
||||
path: { "${params.outdir}/bowtie2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_unmapped,
|
||||
pattern: '*.fastq.gz'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
|
@ -240,10 +282,17 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/bbduk/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{fastq.gz,log}',
|
||||
enabled: params.save_complexityfiltered_reads
|
||||
[
|
||||
path: { "${params.outdir}/bbduk/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{fastq.gz,log}',
|
||||
enabled: params.save_complexityfiltered_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/bbduk/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -255,10 +304,17 @@ process {
|
|||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/prinseqplusplus/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
|
||||
enabled: params.save_complexityfiltered_reads
|
||||
[
|
||||
path: { "${params.outdir}/prinseqplusplus/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
|
||||
enabled: params.save_complexityfiltered_reads
|
||||
],
|
||||
[
|
||||
path: { "${params.outdir}/prinseqplusplus/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.log'
|
||||
]
|
||||
]
|
||||
}
|
||||
|
||||
|
|
@ -295,7 +351,7 @@ process {
|
|||
|
||||
withName: KRAKEN2_KRAKEN2 {
|
||||
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/kraken2/${meta.db_name}/" },
|
||||
mode: params.publish_dir_mode,
|
||||
|
|
@ -305,7 +361,7 @@ process {
|
|||
|
||||
withName: BRACKEN_BRACKEN {
|
||||
errorStrategy = 'ignore'
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/bracken/${meta.db_name}/" },
|
||||
mode: params.publish_dir_mode,
|
||||
|
|
@ -318,7 +374,7 @@ process {
|
|||
publishDir = [
|
||||
path: { "${params.outdir}/bracken/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{txt}'
|
||||
pattern: '*.txt'
|
||||
]
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -73,7 +73,8 @@
|
|||
"falco": {
|
||||
"branch": "master",
|
||||
"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
|
||||
"installed_by": ["modules"]
|
||||
"installed_by": ["modules"],
|
||||
"patch": "modules/nf-core/falco/falco.diff"
|
||||
},
|
||||
"fastp": {
|
||||
"branch": "master",
|
||||
|
|
|
|||
16
modules/nf-core/falco/falco.diff
generated
Normal file
16
modules/nf-core/falco/falco.diff
generated
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
Changes in module 'nf-core/falco'
|
||||
--- modules/nf-core/falco/main.nf
|
||||
+++ modules/nf-core/falco/main.nf
|
||||
@@ -33,7 +33,9 @@
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
- falco $args --threads $task.cpus ${reads}
|
||||
+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
||||
************************************************************
|
||||
4
modules/nf-core/falco/main.nf
generated
4
modules/nf-core/falco/main.nf
generated
|
|
@ -33,7 +33,9 @@ process FALCO {
|
|||
"""
|
||||
} else {
|
||||
"""
|
||||
falco $args --threads $task.cpus ${reads}
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
Loading…
Reference in a new issue