diff --git a/subworkflows/local/reference_indexing_single.nf b/subworkflows/local/reference_indexing_single.nf index 41feced1..e81f8080 100644 --- a/subworkflows/local/reference_indexing_single.nf +++ b/subworkflows/local/reference_indexing_single.nf @@ -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' @@ -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 ]} }