revise-tophat2

tasks/tophat2.wdl

    String idx_prefix
 	File read1
 	File read2
+   String base = basename(read1, ".fq.gz")
    String baseout
    String docker
    String cluster
 
    command {
-      tophat2 -p 8 -G ${gtf} -o baseout ${genome_directory}/${idx_prefix} ${read1} ${read2}
+      tophat2 -p 8 -G ${gtf} -o {base} ${genome_directory}/${idx_prefix} ${read1} ${read2}
    }
    
    runtime { 
    }
 
    output {
-      File accepted_hits = "${baseout}/${baseout}_accepted_hits.bam"
-      File unmapped_bam = "${baseout}/${baseout}_unmapped.bam"
+      File accepted_hits = "${base}/${base}_accepted_hits.bam"
+      File unmapped_bam = "${base}/${base}_unmapped.bam"
    }
 }