Integrate the graphs across samples, to form one merged splicing graph (per gene).
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spladder.wdl 1001B

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  1. task spladder {
  2. String sample_id
  3. Array[File] bam
  4. Array[File] bai
  5. Array[File] pickle
  6. File reference_gtf_file
  7. String docker
  8. String cluster
  9. String disk_size
  10. command <<<
  11. set -o pipefail
  12. set -e
  13. mkdir -p ${sample_id}/spladder_out/spladder
  14. for i in ${sep=" " bam}
  15. do
  16. echo $i >> bam.txt
  17. done
  18. sed ':a ; N;s/\n/,/ ; t a ; ' bam.txt > alignment.txt
  19. for i in ${sep=" " pickle}
  20. do
  21. ln -s $i ${sample_id}/spladder_out/spladder/
  22. ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
  23. done
  24. find . -depth > fileList.txt
  25. >>>
  26. runtime {
  27. docker: docker
  28. cluster: cluster
  29. systemDisk: "cloud_ssd 40"
  30. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  31. }
  32. output {
  33. File fileList = "fileList.txt"
  34. File alignment = "alignment.txt"
  35. File pickle_txt = "pickle.txt"
  36. }
  37. }