Merge pull request #121 from nf-cmgg/genomes/mm10

Add support for mouse genome mm10 for vivar compatibility

Author: matthdsm

conf/igenomes.config

@@ -43,7 +43,21 @@ params {
             dragmap     = "${params.igenomes_base}/Mmusculus/GRCm39/dragmap"
             snap        = "${params.igenomes_base}/Mmusculus/GRCm39/snapaligner"
             star        = "${params.igenomes_base}/Mmusculus/GRCm39/star"
+        }
+        "mm10" {
+            // Genome reference
+            fai         = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fna.fai"
+            fasta       = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fna"
+            dict        = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.dict"
+            gtf         = "${params.igenomes_base}/Mmusculus/mm10/seq/Mus_musculus.GRCm38.102.chr.gtf"
 
+            // Aligner reference
+            bowtie2     = "${params.igenomes_base}/Mmusculus/mm10/bowtie2"
+            bwamem      = "${params.igenomes_base}/Mmusculus/mm10/bwa"
+            bwamem2     = "${params.igenomes_base}/Mmusculus/mm10/bwamem2"
+            dragmap     = "${params.igenomes_base}/Mmusculus/mm10/dragmap"
+            snap        = "${params.igenomes_base}/Mmusculus/mm10/snapaligner"
+            star        = "${params.igenomes_base}/Mmusculus/mm10/star"
         }
         "GRCz11" {
             // Genome reference

workflows/preprocessing.nf

@@ -147,7 +147,7 @@ workflow PREPROCESSING {
             if (meta.organism ==~ /(?i)Homo[\s_]sapiens/) {
                 meta = meta + ["genome":"GRCh38"]
             } else if (meta.organism ==~ /(?i)Mus[\s_]musculus/) {
-                meta = meta + ["genome":"GRCm39"]
+                meta = meta + ["genome":"mm10"]
             } else if (meta.organism ==~/(?i)Danio[\s_]rerio/) {
                 meta = meta + ["genome":"GRCz11"]
             } else {