From f13544de13b9a64fb745fddf8b96fb713e360b3d Mon Sep 17 00:00:00 2001 From: ggabernet Date: Fri, 1 Jul 2022 17:13:48 +0200 Subject: [PATCH 1/2] fix igenomes config ascat --- conf/igenomes.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index f16dc970df..24665185a8 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -37,11 +37,11 @@ params { vep_species = 'homo_sapiens' } 'GATK.GRCh38' { - ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg38.zip" + ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip" ascat_genome = 'hg38' - ascat_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg38.zip" - ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg38.zip" - ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg38.zip" + ascat_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip" + ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip" + ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip" bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/" bwamem2 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/" dragmap = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/" From da892061f173094b24ed174355dd64bfecfa8709 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Fri, 1 Jul 2022 20:41:22 +0200 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1da0c0754b..dabcb7f4b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -108,6 +108,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings - [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests - [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file +- [#615](https://github.com/nf-core/sarek/pull/615) - Fix ASCAT igenomes file paths ### Deprecated