Merge pull request #154 from nf-core/145-dev-branch-works-only-on-the…

…-first-sample convert reference channels from queue to value channel
nf-core · Nov 19, 2024 · 25103d3 · 25103d3
2 parents 370ba86 + 9915cc7
commit 25103d3
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diff --git 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
@@ -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 ]