trnascan.wdl

version 1.0
workflow trnascan {
    input {
        File imgap_input_fasta
        String imgap_project_id
        Int    additional_threads
        String container = "microbiomedata/img-omics@sha256:d5f4306bf36a97d55a3710280b940b89d7d4aca76a343e75b0e250734bc82b71"
    }
  call trnascan_ba {
    input:
      input_fasta = imgap_input_fasta,
      project_id = imgap_project_id,
      threads = additional_threads,
      container=container
  }
  output {
    File gff = trnascan_ba.gff
    File bacterial_out = trnascan_ba.bacterial_out
    File archaeal_out = trnascan_ba.archaeal_out
  }
  meta {
     author: "Brian Foster"
     email: "bfoster@lbl.gov"
     version: "1.0.0"
  }
}

task trnascan_ba {
    input {
        File input_fasta
        String project_id
        String prefix=sub(project_id, ":", "_")
        Int    threads
        String container
    }
  command <<<
     set -euo pipefail
     cp ~{input_fasta} ./~{prefix}_contigs.fna
     /opt/omics/bin/structural_annotation/trnascan-se_trnas.sh ~{prefix}_contigs.fna ~{threads}
  >>>

  runtime {
    time: "9:00:00"
    docker: container
    cpu: threads
    memory: "115G"
  }

  output {
    File bacterial_out = "~{prefix}_trnascan_bacterial.out"
    File archaeal_out  = "~{prefix}_trnascan_archaeal.out"
    File gff = "~{prefix}_trna.gff"
  }
}