Fix input file name and prefix in genomeIndex process - more fixes for …

…#1
guigolab · Jul 12, 2018 · e0b442f · e0b442f
1 parent bb22380
commit e0b442f
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/ipsa.nf b/ipsa.nf
@@ -103,15 +103,15 @@ log.info ""
 if (params.genome =~ /.fa(sta)?$/) {
   process genomeIndex {
     input:
-    file genome from file(params.genome)
+    file("genome.fa") from genomeChan
 
     output:
     set file("${prefix}.dbx"), file("${prefix}.idx") into genomeIdx
 
     script:
-    prefix = genome.name.replace(/.fa/, '')
+    prefix = file(params.genome).name.replaceAll(/.fa(sta)?$/, '')
     """
-    transf -dir ./${genome} -dbx ${prefix}.dbx -idx ${prefix}.idx -exactdir
+    transf -dir ./genome.fa -dbx ${prefix}.dbx -idx ${prefix}.idx -exactdir
     """
   }
 } else {