SAAV/tasks/samtools.wdl

task samtools {
    File sam
    String sample_id
    String bam = sample_id + ".bam"
    String sorted_bam = sample_id + ".sorted.bam"
    String sorted_bam_index = sample_id + ".sorted.bam.bai"
    String docker
    String cluster

    command <<<
       set -o pipefail
       set -e
       nt=$(nproc)
       /opt/conda/bin/samtools view -bS ${sam} > ${bam}
       /opt/conda/bin/samtools sort -@ $nt ${bam} -o ${sorted_bam}
    >>>

    runtime {
       docker: docker
       cluster: cluster
       systemDisk: "cloud_ssd 40"
       dataDisk: "cloud_ssd 200 /cromwell_root/"
    }

    output {
      File out_bam = sorted_bam
    }

}