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qualimapBAMqc.wdl 613B

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  1. task qualimapBAMqc {
  2. File bam
  3. File bai
  4. File regions
  5. String bamname = basename(bam,".bam")
  6. String docker
  7. String cluster_config
  8. String disk_size
  9. command <<<
  10. set -o pipefail
  11. set -e
  12. nt=$(nproc)
  13. /opt/qualimap/qualimap bamqc -bam ${bam} -regions ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G
  14. tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
  15. >>>
  16. runtime {
  17. docker:docker
  18. cluster:cluster_config
  19. systemDisk:"cloud_ssd 40"
  20. dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
  21. }
  22. output {
  23. File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
  24. }
  25. }