Merge pull request #2 from mortazavilab/devel

add multigenome support

Author: Elnazaa

.DS_Store

@@ -5,7 +5,7 @@ The current version of Dogme has been tested on SLURM clusters and on Macs with
 
 | Software | Version |
 |----------|---------|
-| dorado   | 0.9.1   |
+| dorado   | 1.0     |
 | samtools | 1.15.1  |
 | minimap2 | 2.28    |
 | mod_kit  | 0.4.3   |

README.md

@@ -15,7 +15,7 @@ def getParamOrDefault(param, defaultValue) {
 }
 
 // Set the default value at the workflow level
-def dogmeVersion = "1.0"
+def dogmeVersion = "1.1"
 def defaultModDir = "${launchDir}/doradoModels"
 
 workflow {

dogme.nf

@@ -16,8 +16,17 @@ params {
     scriptEnv = "${launchDir}/dogme.profile"
 
     // needs to be modified to match the right genomic reference
-    genomeRef = '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/GRCm39.primary_assembly.genome.fa'
-    annotRef = '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/gencode.vM36.annotation.gtf'
+    // genome_annot_refs = [
+      //[name: 'genome1', genome: '/path/genome1.fa', annot: '/path/annot1.gtf'],
+      //[name: 'genome2', genome: '/path/genome2.fa', annot: '/path/annot2.gtf']
+    //]
+    genome_annot_refs = [
+      [name: 'mm39', 
+      genome: '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/GRCm39.primary_assembly.genome.fa', 
+      annot: '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/gencode.vM36.annotation.gtf'
+      ]
+    ]
+
     kallistoIndex = '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/mm39GencM36_k63.idx'
     t2g = '/share/crsp/lab/seyedam/share/bridge_dRNA/kallistoref/mm39GencM36_k63.t2g'