From 9f7d06147a1645df9f2311aca9c2c54d01d4d31a Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 Jun 2023 13:26:41 +0200 Subject: [PATCH 1/3] Make fasta genome file available by default for IGV --- conf/modules.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 6cbfc39b..cb30b48c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -957,8 +957,7 @@ if (!params.skip_igv) { [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, - pattern: '*.{fa,fasta}', - enabled: params.save_reference + pattern: '*.{fa,fasta}' ] ] } From b7026cb9e653a826b29b907c2d06802fe798e8db Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 Jun 2023 13:27:54 +0200 Subject: [PATCH 2/3] Fix issue with blacklist provided using the blacklist param --- subworkflows/local/prepare_genome.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index ee402632..d6dbffcf 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -77,7 +77,7 @@ workflow PREPARE_GENOME { ch_blacklist = GUNZIP_BLACKLIST ( [ [:], params.blacklist ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions) } else { - ch_blacklist = Channel.of(params.blacklist) + ch_blacklist = Channel.value(file(params.blacklist)) } } @@ -104,7 +104,7 @@ workflow PREPARE_GENOME { ch_gene_bed = GUNZIP_GENE_BED ( [ [:], params.gene_bed ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) } else { - ch_gene_bed = file(params.gene_bed) + ch_gene_bed = Channel.value(file(params.gene_bed)) } } @@ -116,7 +116,7 @@ workflow PREPARE_GENOME { ch_tss_bed = GUNZIP_TSS_BED ( [ [:], params.tss_bed ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_TSS_BED.out.versions) } else { - ch_tss_bed = file(params.tss_bed) + ch_tss_bed = Channel.value(file(params.tss_bed)) } } @@ -216,7 +216,7 @@ workflow PREPARE_GENOME { ch_star_index = UNTAR_STAR_INDEX ( [ [:], params.star_index ] ).untar.map{ it[1] } ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) } else { - ch_star_index = file(params.star_index) + ch_star_index = Channel.value(file(params.star_index)) } } else { ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index From 8f0d882e8770828709dc1d4555415f1f32d60712 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 Jun 2023 16:01:38 +0200 Subject: [PATCH 3/3] Update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9b968e64..ce27dd38 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add public_aws_ecr profile for using containers hosted on ECR. - [[#277](https://github.com/nf-core/atacseq/issues/277)] - Fix error when using a gunziped fasta file. - [[#286](https://github.com/nf-core/atacseq/issues/286)] - Fix error when no `--mito_name parameter is provided. +- [[#268](https://github.com/nf-core/atacseq/issues/268)] - Fix error when a bed file is provided using the `--blacklist` option. +- [[#278](https://github.com/nf-core/atacseq/issues/278)] - Make genome fasta file available when `IGV` process is run. ### Parameters