For RNA-seq data, from bams to AS Information files.
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  1. task samtools {
  2. File bam_file
  3. String bam_id=basename(bam_file)
  4. String docker
  5. String cluster
  6. String disk_size
  7. command <<<
  8. samtools index --help
  9. samtools index -b ${bam_file} > ./${bam_id}.bai
  10. cp ${bam_file} ./
  11. >>>
  12. runtime {
  13. docker: docker
  14. cluster: cluster
  15. systemDisk: "cloud_ssd 40"
  16. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  17. }
  18. output {
  19. File bam="${bam_id}"
  20. File bam_index="${bam_id}.bai"
  21. }
  22. }