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Merge branch 'dev' into porechop-log

This commit is contained in:
James A. Fellows Yates 2022-07-20 14:05:23 +02:00 committed by GitHub
commit 64f01fcfe0
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4 changed files with 11 additions and 3 deletions

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@ -37,7 +37,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"filtlong": {
"git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
"git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
},
"gunzip": {
"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"

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@ -12,6 +12,7 @@ process FILTLONG {
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -27,6 +28,7 @@ process FILTLONG {
$short_reads \\
$args \\
$longreads \\
2> ${prefix}.log \\
| gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml

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@ -45,6 +45,11 @@ output:
type: file
description: Filtered (compressed) fastq file
pattern: "*.fastq.gz"
- log:
type: file
description: Standard error logging file containing summary statistics
pattern: "*.log"
authors:
- "@d4straub"
- "@sofstam"

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@ -32,6 +32,7 @@ workflow LONGREAD_PREPROCESSING {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} else {
PORECHOP ( reads )
@ -48,7 +49,7 @@ 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.collect{it[1]}.ifEmpty([]) )
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log.collect{it[1]}.ifEmpty([]) )
}
FASTQC_PROCESSED ( ch_processed_reads )