rnaseq-engineering/workflow.wdl

import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/fastp.wdl" as fastp
import "./tasks/qualimap.wdl" as qualimap
import "./tasks/hisat2.wdl" as hisat2
import "./tasks/samtools.wdl" as samtools
import "./tasks/stringtie.wdl" as stringtie
import "./tasks/ballgown.wdl" as ballgown
import "./tasks/count.wdl" as count

workflow {{ project_name }} {
  File read1
  File read2
  File idx
  File screen_ref_dir
  File fastq_screen_conf
  File gtf

  String disk_size
  String fastqc_docker
  String fastqc_cluster
  String fastqscreen_docker
  String fastqscreen_cluster
  String fastp_docker
  String fastp_cluster
  String adapter_sequence
  String adapter_sequence_r2
  String hisat2_docker
  String hisat2_cluster
  String idx_prefix
  String stringtie_docker
  String stringtie_cluster
  String samtools_docker
  String samtools_cluster
  String qualimap_docker
  String qualimap_cluster
  String ballgown_docker
  String ballgown_cluster
  String count_docker
  String count_cluster
  String count_length
  String sample_id

  Int insert_size

  Boolean pre_alignment_qc
  Boolean qualimap_qc
  Boolean trim_adapter
  
  if (pre_alignment_qc) {
    call fastqc.fastqc as fastqc {
      input:
      read1=read1,
      read2=read2,
      docker=fastqc_docker,
      cluster=fastqc_cluster,
      disk_size=disk_size
    }
    
    call fastqscreen.fastqscreen as fastqscreen {
      input:
      read1=read1,
      read2=read2,
      docker=fastqscreen_docker,
      cluster=fastqscreen_cluster,
      screen_ref_dir=screen_ref_dir,
      fastq_screen_conf=fastq_screen_conf,
      disk_size=disk_size
    }	
  }

  call fastp.fastp as fastp {
    input:
    read1=read1,
    read2=read2,
    docker=fastp_docker,
    cluster=fastp_cluster,
    disk_size=disk_size,
    adapter_sequence=adapter_sequence,
    adapter_sequence_r2=adapter_sequence_r2,
    trim_adapter=trim_adapter
  }
      
  call hisat2.hisat2 as hisat2 {
    input:
    docker=hisat2_docker,
    cluster=hisat2_cluster,
    idx=idx,
    idx_prefix=idx_prefix,
    read_1P=fastp.trim_R1,
    read_2P=fastp.trim_R2,
    disk_size=disk_size
  }
  
  call samtools.samtools as samtools {
    input:
    docker=samtools_docker,
    cluster=samtools_cluster,
    sam=hisat2.sam,
    insert_size=insert_size,
    disk_size=disk_size
  }

  if (qualimap_qc){
    call qualimap.qualimap as qualimap {
      input:
      bam=samtools.out_sort_bam,
      gtf=gtf,
      docker=qualimap_docker,
      cluster=qualimap_cluster,
      disk_size=disk_size
    }
  }

  call stringtie.stringtie as stringtie {
    input:
    docker=stringtie_docker,
    cluster=stringtie_cluster,
    gtf=gtf,
    bam=samtools.out_sort_bam,
    disk_size=disk_size
  }

  call ballgown.ballgown as ballgown {
    input:
    docker=ballgown_docker,
    cluster=ballgown_cluster,
    ballgown=stringtie.ballgown,
    gene_abundance=stringtie.gene_abundance,
    disk_size=disk_size
  }
  
  call count.count as count {
    input:
    docker=count_docker,
    cluster=count_cluster,
    ballgown=stringtie.ballgown,
    gene_abundance=stringtie.gene_abundance,
    disk_size=disk_size,
    count_length=count_length
  }
}