For RNA-seq data, from bam/fastq to AS sites files.
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

rmats.wdl 1008B

4 years ago
4 years ago
4 years ago
4 years ago
4 years ago
123456789101112131415161718192021222324252627282930313233343536373839404142434445
  1. task rmats {
  2. String sample_id
  3. File b1_txt
  4. File b2_txt
  5. File reference_gtf_file
  6. String docker
  7. String cluster
  8. String disk_size
  9. command <<<
  10. set -o pipefail
  11. set -e
  12. mkdir -p ${sample_id}/output
  13. mkdir -p ${sample_id}/tmp_output
  14. python /usr/local/bin/rmats.py --b1 ${b1_txt} \
  15. --b2 ${b2_txt} \
  16. --gtf ${reference_gtf_file} \
  17. -t paired \
  18. --readLength 150 \
  19. --nthread 4 \
  20. --od ${sample_id}/output \
  21. --tmp ${sample_id}/tmp_output
  22. find . -depth > fileList.txt
  23. >>>
  24. runtime {
  25. docker: docker
  26. cluster: cluster
  27. systemDisk: "cloud_ssd 40"
  28. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  29. }
  30. output {
  31. File fileList = "fileList.txt"
  32. Array[File] AS_txt = glob("${sample_id}/output/*.txt")
  33. Array[File] tmp = glob("${sample_id}/output/tmp/*")
  34. }
  35. }