From 9915cc7503bbdb92e8f061c18e04e79bb13bee17 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Fri, 15 Nov 2024 08:25:56 +0000 Subject: [PATCH] convert reference channels from queue to value channel --- CHANGELOG.md | 1 + subworkflows/local/prepare_genome/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cbd58e5..3256a11 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` - [#144](https://github.com/nf-core/rnavar/pull/144) - Change gatk_vf params from integer to floats +- [#145](https://github.com/nf-core/rnavar/issues/145) - Converted `star_index` and `gtf` emit channels from queue to value channels in `PREPARE_GENOME` subworkflow - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf ### Dependencies diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index a568e1a..e5d9c8c 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -70,8 +70,8 @@ workflow PREPARE_GENOME { exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed fasta = ch_fasta fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai - gtf = ch_gtf // path: genome.gtf - star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ + gtf = ch_gtf.first() // path: genome.gtf + star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi versions = ch_versions // channel: [ versions.yml ]