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Fix filtlong logs

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This commit is contained in:
sofstam 2022-07-19 14:01:11 +02:00
parent 1ba6a08135
commit 526ed79763
1 changed files with 5 additions and 4 deletions
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9
subworkflows/local/longread_preprocessing.nf
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@ -12,7 +12,7 @@ workflow LONGREAD_PREPROCESSING {
main: main:
ch_versions = Channel.empty() ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty() = Channel.empty()
if ( params.longread_qc_run_clip && !params.longread_qc_run_filter ) { if ( params.longread_qc_run_clip && !params.longread_qc_run_filter ) {
PORECHOP ( reads ) PORECHOP ( reads )
@ -30,6 +30,7 @@ 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 = .mix( FILTLONG.out.log.collect{it[1]}.ifEmpty([]))
} else { } else {
PORECHOP ( reads ) PORECHOP ( reads )
@ -45,16 +46,16 @@ 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( FILTLONG.out.log.collect{it[1]}.ifEmpty([]))
} }
FASTQC_PROCESSED ( ch_processed_reads ) FASTQC_PROCESSED ( ch_processed_reads )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) = .mix( FASTQC_PROCESSED.out.zip )
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log.collect{it[1]}.ifEmpty([]))
emit: emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ] reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files mqc =
} }