From e03bc464f52f1ab31a149b66ad8f12e1ec175127 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 23 Oct 2024 14:56:26 +0000 Subject: [PATCH 1/3] add hisat2 bismark index to igenomes --- conf/igenomes.config | 25 +++++++++++++------------ main.nf | 2 +- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 8cf56cd0..3edfaa7e 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -27,18 +27,19 @@ params { blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" } 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - fasta_index = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - bwameth = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BwamethIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" + bismark_hisat2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/Hisat2Index/" + bwameth = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BwamethIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } 'CHM13' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" diff --git a/main.nf b/main.nf index c8386bed..5c1056c8 100644 --- a/main.nf +++ b/main.nf @@ -28,8 +28,8 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_meth */ params.fasta = getGenomeAttribute('fasta') params.fasta_index = getGenomeAttribute('fasta_index') -params.bismark_index = getGenomeAttribute('bismark') params.bwameth_index = getGenomeAttribute('bwameth') +params.bismark_index = params.aligner == 'bismark_hisat' ? getGenomeAttribute('bismark_hisat2') : getGenomeAttribute('bismark') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 5e7fca3c609e06b283be337d1ed2b3904eb8d276 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 23 Oct 2024 15:03:06 +0000 Subject: [PATCH 2/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c6cec0d..0eb61f55 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ - 🔧 Removed `conf/modules.config` and introduce separate `nextflow.config` [#414](https://github.com/nf-core/methylseq/pull/414) - 🔧 Added sub-workflow & pipeline level nf-tests [#414](https://github.com/nf-core/methylseq/pull/414) - 🔧 Pipeline metro map added by @Shaun-Regenbaum , @FelixKrueger , @ewels [#438](https://github.com/nf-core/methylseq/pull/438) +- 🔧 Add Bismark Hisat2 index to igenomes [#444](https://github.com/nf-core/methylseq/pull/444) ## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05 From 96fb9ec24ad4a886e2ad4e84efb03cbdb1de807d Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Wed, 23 Oct 2024 20:35:49 +0530 Subject: [PATCH 3/3] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0eb61f55..429f463f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,7 @@ - 🔧 Removed `conf/modules.config` and introduce separate `nextflow.config` [#414](https://github.com/nf-core/methylseq/pull/414) - 🔧 Added sub-workflow & pipeline level nf-tests [#414](https://github.com/nf-core/methylseq/pull/414) - 🔧 Pipeline metro map added by @Shaun-Regenbaum , @FelixKrueger , @ewels [#438](https://github.com/nf-core/methylseq/pull/438) -- 🔧 Add Bismark Hisat2 index to igenomes [#444](https://github.com/nf-core/methylseq/pull/444) +- 🔧 Add Bismark HISAT2 index to igenomes [#444](https://github.com/nf-core/methylseq/pull/444) ## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05