public_health_viral_genomics/workflows/wf_ncbi_scrub_pe.wdl at main · theiagen/public_health_viral_genomics · GitHub

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version 1.0

import "../tasks/task_read_clean.wdl" as read_clean
import "../tasks/task_taxonID.wdl" as taxonID
import "../tasks/task_versioning.wdl" as versioning

workflow dehost_pe {
  input {
    String samplename
    File read1
    File read2
  }
  call read_clean.ncbi_scrub_pe {
    input:
      samplename = samplename,
      read1 = read1,
      read2 = read2
  }
  call taxonID.kraken2 {
    input:
      samplename = samplename,
      read1 = ncbi_scrub_pe.read1_dehosted,
      read2 = ncbi_scrub_pe.read2_dehosted
  }
  call versioning.version_capture{
    input:
  }
  output {
    String ncbi_scrub_pe_version = version_capture.phvg_version
    String ncbi_scrub_se_analysis_date = version_capture.date
    File read1_dehosted = ncbi_scrub_pe.read1_dehosted
    File read2_dehosted = ncbi_scrub_pe.read2_dehosted
    Int read1_human_spots_removed = ncbi_scrub_pe.read1_human_spots_removed
    Int read2_human_spots_removed = ncbi_scrub_pe.read2_human_spots_removed
    String ncbi_scrub_docker = ncbi_scrub_pe.ncbi_scrub_docker
    Float kraken_human_dehosted = kraken2.percent_human
    Float kraken_sc2_dehosted = kraken2.percent_sc2
    String kraken_report_dehosted = kraken2.kraken_report
    String kraken_version_dehosted = kraken2.version
  }
}