Handle different versions of vep and different vep cache locations

viklund · viklund · commit 0821f93b8c1b · 2017-08-18T17:54:38.000+02:00
diff --git a/config/bianca.config b/config/bianca.config
@@ -1,3 +1,4 @@
+params.vep_cache_version = 89
 process {
     $index_bamfile {
         module = ['bioinfo-tools', 'samtools/1.3']
@@ -37,7 +38,7 @@ process {
 
     $variant_effect_predictor {
         cpus = 4
-        module = ['bioinfo-tools', 'vep/84']
+        module = ['bioinfo-tools', 'vep/89']
     }
 
     $snpEff {
diff --git a/config/milou.config b/config/milou.config
@@ -1,3 +1,4 @@
+params.vep_cache_version = 84
 process {
     $index_bamfile {
         module = ['bioinfo-tools', 'samtools/1.3']
diff --git a/main.nf b/main.nf
@@ -353,7 +353,7 @@ process variant_effect_predictor {
     """
     INFILE="$infile"
     OUTFILE="\${INFILE%.vcf}.vep.vcf"
-    VEP_CACHE="/sw/data/uppnex/vep/84"
+    VEP_CACHE="/sw/data/uppnex/vep/$params.vep_cache_version"
     ASSEMBLY="$params.assembly"
 
     case "\$INFILE" in

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+params.vep_cache_version = 84`
`1`	`2`	`process {`
`2`	`3`	`$index_bamfile {`
`3`	`4`	`module = ['bioinfo-tools', 'samtools/1.3']`