SplAdder/tasks/samtools.wdl

task samtools {
    File bam_file
    String bam_id=basename(bam_file)
    String docker
    String cluster
    String disk_size


    command <<<
       samtools index --help
       samtools index -b ${bam_file} > ./${bam_id}.bai
       cp ${bam_file} ./                               
    >>>

    runtime {
       docker: docker
       cluster: cluster
       systemDisk: "cloud_ssd 40"
       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
      File bam="${bam_id}"      
      File bam_index="${bam_id}.bai"
    }

}