revise-tophat

tasks/tophat2.wdl

@@ -9,7 +9,7 @@ task tophat2 {
    String cluster
 
    command <<<
-      tophat -p 8 -G ${gtf} -o ${genome_directory}/${idx_prefix} ${read1} ${read2}
+      tophat -p 8 -G ${gtf} -o baseout ${genome_directory}/${idx_prefix} ${read1} ${read2}
    >>>
    
    runtime { 
@@ -20,7 +20,7 @@ task tophat2 {
    }
 
    output {
-      File accepted_hits = "${baseout}_accepted_hits.bam"
-      File unmapped_bam = "${baseout}_unmapped.bam"
+      File accepted_hits = baseout + "_accepted_hits.bam"
+      File unmapped_bam = baseout + "_unmapped.bam"
    }
 }