rnaseq-engineering/workflow.wdl

import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
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
	String idx_prefix
	File gtf
	String disk_size
	String fastqc_docker
	String fastqc_cluster
	String fastqscreen_docker
	String fastqscreen_cluster
	String hisat2_docker
	String hisat2_cluster
	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

	Boolean pre_alignment_qc
	
	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 hisat2.hisat2 as hisat2 {
		input: 
		docker = hisat2_docker,
		cluster = hisat2_cluster,
		idx=idx, 
		idx_prefix=idx_prefix, 
		read_1P=read1, 
		read_2P=read2,
		disk_size= disk_size
		}

	call samtools.samtools as samtools {
		input: 
		docker = samtools_docker,
		cluster = samtools_cluster,
		sam = hisat2.sam,
		disk_size= disk_size
		}

	call qualimap.qualimap as qualimap {
		input:
		bam = samtools.out_bam,
		bai = samtools.out_bam_index,
		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_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: 
		sample_id = sample_id,
		docker = count_docker,
		cluster = count_cluster,
		ballgown = stringtie.ballgown,
		disk_size = disk_size,
		count_length = count_length
	}
}