revise-tophat

tasks/tophat2.wdl

    String idx_prefix
 	File read1
 	File read2
-   String base = basename(read1, ".fq.gz")
    String baseout
    String docker
    String cluster
 
    command <<<
-      tophat -p 8 -G ${gtf} -o ${base} ${genome_directory}/${idx_prefix} ${read1} ${read2}
+      tophat -p 8 -G ${gtf} -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2}
    >>>
    
    runtime { 
    }
 
    output {
-      File accepted_hits = "${base}/${base}_accepted_hits.bam"
-      File unmapped_bam = "${base}/${base}_unmapped.bam"
+      File accepted_hits = "${baseout}/${baseout}_accepted_hits.bam"
+      File unmapped_bam = "${baseout}/${babaseoutse}_unmapped.bam"
    }
 }