Merge pull request #856 from maxulysse/dev_add_R64-1-1

Add R64-1-1 and UMD3.1
nf-core · Nov 21, 2022 · 6d24c73 · 6d24c73
2 parents 740127f + e11b18e
commit 6d24c73
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [#856](https://github.com/nf-core/sarek/pull/856) - Add annotation for `R64-1-1` and `UMD3.1`
+
 ### Changed
 
 - [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -138,6 +138,13 @@ params {
             bwa                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            snpeff_db             = 'UMD3.1.75'
+            snpeff_genome         = 'UMD3.1'
+            snpeff_version        = '5.1'
+            vep_cache_version     = 94
+            vep_genome            = 'UMD3.1'
+            vep_species           = 'bos_taurus'
+            vep_version           = '106.1'
         }
         'WBcel235' {
             bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
@@ -214,6 +221,13 @@ params {
         'R64-1-1' {
             bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db             = 'R64-1-1.105'
+            snpeff_genome         = 'R64-1-1'
+            snpeff_version        = '5.1'
+            vep_cache_version     = 106
+            vep_genome            = 'R64-1-1'
+            vep_species           = 'saccharomyces_cerevisiae'
+            vep_version           = '106.1'
         }
         'EF2' {
             bwa                   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"