millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 01:16:03 +00:00
Code Issues Releases Packages Activity

style: use map addition instead of cloning

Browse source
This commit is contained in:
Moritz E. Beber 2023-03-07 13:40:21 +01:00
parent d17dce5590
commit 07db3c93e2
1 changed files with 4 additions and 14 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
subworkflows/local/longread_preprocessing.nf
View file

@ -20,33 +20,23 @@ workflow LONGREAD_PREPROCESSING {
PORECHOP_PORECHOP ( reads ) PORECHOP_PORECHOP ( reads )
ch_processed_reads = PORECHOP_PORECHOP.out.reads ch_processed_reads = PORECHOP_PORECHOP.out.reads
.map { .map { meta, reads -> [ meta + [single_end: 1], reads ] }
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log ) ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) { } else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
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 ) ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} else { } else {
PORECHOP_PORECHOP ( reads ) PORECHOP_PORECHOP ( reads )
ch_clipped_reads = PORECHOP_PORECHOP.out.reads ch_clipped_reads = PORECHOP_PORECHOP.out.reads
.map { .map { meta, reads -> [ meta + [single_end: 1], reads ] }
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads ch_processed_reads = FILTLONG ( ch_clipped_reads.map { meta, reads -> [meta, [], reads ] } ).reads
ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first()) ch_versions = ch_versions.mix(FILTLONG.out.versions.first())