Nevar pievienot vairāk kā 25 tēmas Tēmai ir jāsākas ar burtu vai ciparu, tā var saturēt domu zīmes ('-') un var būt līdz 35 simboliem gara.

spladder_merge.wdl 1.6KB

pirms 3 gadiem
pirms 3 gadiem
pirms 3 gadiem
pirms 3 gadiem
pirms 3 gadiem
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  1. task spladder_merge {
  2. String sample_id
  3. File bam
  4. File pickle
  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}/spladder_out/spladder
  13. ln -s ${bam}/*.bam ./
  14. ls ./ | grep bam$ > alignment.txt
  15. ln -s ${bam}/*.bai ./
  16. ls ./ | grep bai$ > alignment_bai.txt
  17. ln -s ${pickle}/*.pickle ${sample_id}/spladder_out/spladder/
  18. ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
  19. nt=$(nproc)
  20. spladder build -o ${sample_id}/spladder_out \
  21. --annotation ${reference_gtf_file} \
  22. --bams alignment.txt \
  23. --confidence 2 \
  24. --merge-strat merge_graphs \
  25. --readlen 150 \
  26. --parallel $nt \
  27. --event-types exon_skip
  28. find . -depth > fileList.txt
  29. >>>
  30. runtime {
  31. docker: docker
  32. cluster: cluster
  33. systemDisk: "cloud_ssd 500"
  34. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  35. timeout: 129600
  36. }
  37. output {
  38. File fileList = "fileList.txt"
  39. File alignment = "alignment.txt"
  40. File alignment_bai = "alignment_bai.txt"
  41. File pickle_txt = "pickle.txt"
  42. Array[File] AS_gff = glob("${sample_id}/spladder_out/*.gff3")
  43. Array[File] AS_gz = glob("${sample_id}/spladder_out/*.gz")
  44. Array[File] spladder_out = glob("${sample_id}/spladder_out/*")
  45. Array[File] spladder = glob("${sample_id}/spladder_out/spladder/*")
  46. }
  47. }