stringtie_md5/workflow.wdl

import "./tasks/fastp.wdl" as fastp
import "./tasks/hisat2.wdl" as hisat2
import "./tasks/samtools.wdl" as samtools
import "./tasks/stringtie.wdl" as stringtie
import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
import "./tasks/qualimapRNAseq.wdl" as qualimapRNAseq
import "./tasks/ballgown.wdl" as ballgown
import "./tasks/count.wdl" as count
import "./tasks/MD5.wdl" as MD5

workflow {{ project_name }} {
	File bam
	File idx
	File screen_ref_dir
	File fastq_screen_conf
	File gtf
	String sample_id
	String fastp_docker
	String adapter_sequence
	String adapter_sequence_r2
	String fastp_cluster
	String umi_loc
	String idx_prefix
	String pen_intronlen
	String fastqc_cluster_config
	String fastqc_docker
	String fastqscreen_docker
	String fastqscreen_cluster_config
	String hisat2_docker
	String hisat2_cluster
	String qualimapBAMqc_docker
	String qualimapBAMqc_cluster_config
	String qualimapRNAseq_docker
	String qualimapRNAseq_cluster_config
	String samtools_docker
	String samtools_cluster
	String stringtie_docker
	String stringtie_cluster
	String multiqc_cluster_config
	String multiqc_docker
	Int multiqc_disk_size
	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 pen_cansplice
	Int pen_noncansplice
	Int min_intronlen
	Int max_intronlen
	Int maxins
	Int minins
	Int fastqc_disk_size
	Int fastqscreen_disk_size
	Int qualimapBAMqc_disk_size
	Int qualimapRNAseq_disk_size
	Int insert_size
	Int minimum_length_allowed_for_the_predicted_transcripts
	Int Junctions_no_spliced_reads
	Int count_length
	Float minimum_isoform_abundance
	Float maximum_fraction_of_muliplelocationmapped_reads
	String ballgown_docker
	String ballgown_cluster
	String disk_size
	String count_docker
	String count_cluster
	String docker
	String cluster_config


	call stringtie.stringtie as stringtie {
		input: 
		sample_id = sample_id,
		gtf = gtf, 
		bam = bam,
		docker = stringtie_docker,
		cluster = stringtie_cluster,
		disk_size = disk_size,
		minimum_length_allowed_for_the_predicted_transcripts = minimum_length_allowed_for_the_predicted_transcripts,
		Junctions_no_spliced_reads = Junctions_no_spliced_reads,
		minimum_isoform_abundance = minimum_isoform_abundance,
		maximum_fraction_of_muliplelocationmapped_reads = maximum_fraction_of_muliplelocationmapped_reads
	}

	call MD5.MD5 as MD5 {
		input:
		file1 = stringtie.covered_transcripts,
		file2 = stringtie.gene_abundance,
		docker = docker,
		disk_size = disk_size,
		cluster_config=cluster_config
	}
}