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_fp.wdl" as hisat2_fp
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_fp.hisat2_fp as hisat2_fp {
			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:
			sample_id=sample_id,
			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
	}
}