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convert reference channels from queue to value channel #154

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Nov 19, 2024
Merged

convert reference channels from queue to value channel #154

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions subworkflows/local/prepare_genome/main.nf
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Expand Up @@ -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 ]
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