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Merge pull request #106 from nf-core/porechop-log

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Add emitting porechop logs to multiqc and fix collection of others
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James A. Fellows Yates 2022-07-29 10:58:12 +02:00 committed by GitHub
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 459 additions and 5 deletions
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2
modules.json
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@ -88,7 +88,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
"git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
},
"prinseqplusplus": {
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"

4
modules/nf-core/modules/porechop/main.nf generated
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@ -12,6 +12,7 @@ process PORECHOP {
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -25,7 +26,8 @@ process PORECHOP {
-i $reads \\
-t $task.cpus \\
$args \\
-o ${prefix}.fastq.gz
-o ${prefix}.fastq.gz \\
> ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":

5
modules/nf-core/modules/porechop/meta.yml generated
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@ -38,6 +38,10 @@ output:
type: file
description: Demultiplexed and/or adapter-trimmed fastq.gz file
pattern: "*.{fastq.gz}"
- log:
type: file
description: Log file containing stdout information
pattern: "*.log"
authors:
- "@ggabernet"
@ -48,3 +52,4 @@ authors:
- "@jonasscheid"
- "@jonoave"
- "@GokceOGUZ"
- "@jfy133"

6
subworkflows/local/longread_preprocessing.nf
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@ -23,9 +23,11 @@ workflow LONGREAD_PREPROCESSING {
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
}
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
} else if ( !params.longread_qc_run_clip && params.longread_qc_run_filter ) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
@ -46,8 +48,8 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
}
FASTQC_PROCESSED ( ch_processed_reads )