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Merge branch 'dev' into porechop-log

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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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2
modules.json
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@ -37,7 +37,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"filtlong": { "filtlong": {
"git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1" "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
}, },
"gunzip": { "gunzip": {
"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9" "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"

4
modules/nf-core/modules/filtlong/main.nf generated
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@ -12,7 +12,8 @@ process FILTLONG {
output: output:
tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -27,6 +28,7 @@ process FILTLONG {
$short_reads \\ $short_reads \\
$args \\ $args \\
$longreads \\ $longreads \\
2> ${prefix}.log \\
| gzip -n > ${prefix}.fastq.gz | gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

5
modules/nf-core/modules/filtlong/meta.yml generated
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@ -45,6 +45,11 @@ output:
type: file type: file
description: Filtered (compressed) fastq file description: Filtered (compressed) fastq file
pattern: "*.fastq.gz" pattern: "*.fastq.gz"
- log:
type: file
description: Standard error logging file containing summary statistics
pattern: "*.log"
authors: authors:
- "@d4straub" - "@d4straub"
- "@sofstam"

3
subworkflows/local/longread_preprocessing.nf
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@ -32,6 +32,7 @@ workflow LONGREAD_PREPROCESSING {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} ) ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
ch_versions = ch_versions.mix(FILTLONG.out.versions.first()) ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} else { } else {
PORECHOP ( reads ) PORECHOP ( reads )
@ -48,7 +49,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.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( 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 ) FASTQC_PROCESSED ( ch_processed_reads )