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ensure single_ref gunzip gets correct configureation
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TCLamnidis committed Feb 14, 2025
1 parent 66531d1 commit 4e52dc3
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions subworkflows/local/reference_indexing_single.nf
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
//
include { grabUngzippedExtension } from '../../subworkflows/local/utils_nfcore_eager_pipeline/main'

include { GUNZIP } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/gunzip/main'
include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main'
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main'
Expand All @@ -27,9 +27,9 @@ workflow REFERENCE_INDEXING_SINGLE {
// Detect if fasta is gzipped or not, unzip if necessary, and generate meta ID by sanitizing file
if ( fasta.extension == 'gz' ) {
ch_gz_ref = Channel.fromPath(fasta).map{[[], it]}
GUNZIP ( ch_gz_ref )
ch_ungz_ref = GUNZIP.out.gunzip.map{[[id: clean_name], it[1] ]}
ch_versions = ch_versions.mix( GUNZIP.out.versions.first())
GUNZIP_FASTA ( ch_gz_ref )
ch_ungz_ref = GUNZIP_FASTA.out.gunzip.map{[[id: clean_name], it[1] ]}
ch_versions = ch_versions.mix( GUNZIP_FASTA.out.versions.first())
} else {
ch_ungz_ref = Channel.fromPath(fasta).map{[[id: clean_name], it ]}
}
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