Merge pull request #444 from sateeshperi/dev

add hisat2 bismark index to igenomes
nf-core · Oct 23, 2024 · 0bbf07f · 0bbf07f
2 parents d7578f0 + 96fb9ec
commit 0bbf07f
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Showing 3 changed files with 15 additions and 13 deletions.
diff --git 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
 

diff --git 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
@@ -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')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~