prepare junction bed and gtf with novel transcripts for PGA input
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.

23 line
448B

  1. task stringtie {
  2. File bam
  3. File anno_gtf
  4. String docker
  5. String sample_id
  6. String cluster
  7. command <<<
  8. nt=$(nproc)
  9. /opt/conda/bin/stringtie -p $nt -G ${anno_gtf} -o ${sample_id}.gtf -l CUFF ${bam}
  10. >>>
  11. runtime {
  12. docker: docker
  13. cluster: cluster
  14. systemDisk: "cloud_ssd 40"
  15. dataDisk: "cloud_ssd 150 /cromwell_root/"
  16. }
  17. output {
  18. File gtf = "${sample_id}.gtf"
  19. }
  20. }