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ch_fasta_fai and ch_gtf fix after nf-core/tools v2.14.1 merge #149

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Jun 27, 2024
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ch_fasta_fai and ch_gtf fix after nf-core/tools v2.14.1 merge #149

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c52ab26
Updated ch_gtf channel in main.nf
nschcolnicov Jun 26, 2024
ccd9d82
Updated ch_fasta_fai channel
nschcolnicov Jun 26, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF
- [#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`
- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf

### Dependencies

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5 changes: 2 additions & 3 deletions main.nf
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Expand Up @@ -111,14 +111,13 @@ workflow NFCORE_RNAVAR {

ch_fasta = PREPARE_GENOME.out.fasta
ch_star_index = PREPARE_GENOME.out.star_index
ch_gtf = PREPARE_GENOME.out.gtf
ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
: PREPARE_GENOME.out.dict
ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect()
ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai)
: PREPARE_GENOME.out.fasta_fai
ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect()
: PREPARE_GENOME.out.exon_bed
ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ it -> [ [id:'gtf'], it ] }.collect()
: PREPARE_GENOME.out.gtf
ch_dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect()
: PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect()
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