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

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version 1.0

import "../tasks/quality_control/task_fastq_scan.wdl" as fastq_scan
import "../tasks/task_read_clean.wdl" as read_clean
import "../tasks/task_taxonID.wdl" as taxonID

workflow read_QC_trim {
  meta {
    description: "Runs basic QC (fastq-scan), trimming (SeqyClean), and taxonomic ID (Kraken2) on illumina PE reads"
  }
  input {
    String samplename
    File read1_raw
    Int? trimmomatic_minlen = 25
    Int? trimmomatic_quality_trim_score = 30
    Int? trimmomatic_window_size = 4
    Int  bbduk_mem = 8
    String? target_org
    File? adapters
    File? phix
    String? trim_args
  }
# Commented out as NCBI SCRUB not currently compatible with 75bp SE data used in SC2 sequencing
#  call read_clean.ncbi_scrub_se {
#    input:
#      samplename = samplename,
#      read1 = read1_raw
#  }
  call read_clean.trimmomatic_se {
    input:
      samplename = samplename,
      read1 = read1_raw,
      trimmomatic_minlen = trimmomatic_minlen,
      trimmomatic_quality_trim_score = trimmomatic_quality_trim_score,
      trimmomatic_window_size = trimmomatic_window_size,
      trimmomatic_args = trim_args
  }
  call read_clean.bbduk_se {
    input:
      samplename = samplename,
      read1_trimmed = trimmomatic_se.read1_trimmed,
      memory = bbduk_mem,
      adapters = adapters,
      phix = phix
  }
  call fastq_scan.fastq_scan_se as fastq_scan_raw {
    input:
      read1 = read1_raw
  }
  call fastq_scan.fastq_scan_se as fastq_scan_clean {
    input:
      read1 = bbduk_se.read1_clean
  }
  call taxonID.kraken2 as kraken2_raw {
    input:
      samplename = samplename,
      read1 = bbduk_se.read1_clean,
      target_org = target_org
  }
#  call taxonID.kraken2 as kraken2_dehosted {
#    input:
#      samplename = samplename,
#      read1 = ncbi_scrub_se.read1_dehosted
#  }
  output {
    File read1_clean = bbduk_se.read1_clean
    Int fastq_scan_number_reads = fastq_scan_raw.read1_seq
    Int fastq_scan_clean_number_reads = fastq_scan_clean.read1_seq
    String kraken_version = kraken2_raw.version
    Float kraken_human = kraken2_raw.percent_human
    Float kraken_sc2 = kraken2_raw.percent_sc2
    String? kraken_target_org = kraken2_raw.percent_target_org
    File kraken_report = kraken2_raw.kraken_report
    String? kraken_target_org_name = target_org
#    Float    kraken_human_dehosted    =    kraken2_dehosted.percent_human
#    Float    kraken_sc2_dehosted    =    kraken2_dehosted.percent_sc2
#    String    kraken_report_dehosted    =    kraken2_dehosted.kraken_report
    String fastq_scan_version = fastq_scan_raw.version
    String bbduk_docker = bbduk_se.bbduk_docker
    String trimmomatic_version = trimmomatic_se.version
  }
}