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 umi_loc
	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 trim_front1 
	Int trim_tail1 
	Int max_len1 
	Int trim_front2 
	Int trim_tail2  
	Int max_len2 
	Int disable_adapter_trimming
	Int length_required
	Int umi_len
	Int UMI
	Int qualified_quality_phred
	Int length_required1
	Int disable_quality_filtering
    Int insert_size

	Boolean pre_alignment_qc
	Boolean qualimap_qc
	Boolean fastp_run
	
	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
		}	
	}
	
	if (fastp_run){

		call fastp.fastp as fastp {
		input: 
		sample_id=sample_id, 
		read1=read1, 
		read2=read2,
		docker=fastp_docker,
		cluster=fastp_cluster,
		disk_size=disk_size,
		adapter_sequence=adapter_sequence,
		adapter_sequence_r2=adapter_sequence_r2,
		umi_loc=umi_loc,
		trim_front1=trim_front1,
		trim_tail1=trim_tail1, 
		max_len1=max_len1,
		trim_front2=trim_front2,
		trim_tail2=trim_tail2,
		max_len2=max_len2,
		disable_adapter_trimming=disable_adapter_trimming,
		length_required=length_required,
		umi_len=umi_len,
		UMI=UMI,
		qualified_quality_phred=qualified_quality_phred,
		length_required1=length_required1,
		disable_quality_filtering=disable_quality_filtering
		}

		call hisat2.hisat2 as hisat2 {
		input: 
		sample_id=sample_id, 
		idx=idx, 
		idx_prefix=idx_prefix, 
		read_1P=fastp.Trim_R1, 
		read_2P=fastp.Trim_R2,
		docker=hisat2_docker,
		cluster=hisat2_cluster,
		disk_size=disk_size
	}
	}

	if (!fastp_run){
		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,
		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: 
		sample_id=sample_id,
		docker=count_docker,
		cluster=count_cluster,
		ballgown=stringtie.ballgown,
		disk_size=disk_size,
		count_length=count_length
	}
}