From c52ab2630471417dbfd32bfa7c9e4f7ed8bc4697 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 14:46:21 +0000 Subject: [PATCH 1/2] Updated ch_gtf channel in main.nf --- CHANGELOG.md | 1 + main.nf | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bd6b75..0a5d8b5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 channel emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index 6e638a8..ab40a8b 100644 --- a/main.nf +++ b/main.nf @@ -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() : 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() From ccd9d82c1c29771e37ffb8a83a3d1a67d88f32c9 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 20:59:46 +0000 Subject: [PATCH 2/2] Updated ch_fasta_fai channel --- CHANGELOG.md | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a5d8b5..32a5a0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +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 channel emitted by main.nf +- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index ab40a8b..cd9d100 100644 --- a/main.nf +++ b/main.nf @@ -114,7 +114,7 @@ workflow NFCORE_RNAVAR { 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