更新 'workflow.wdl'

workflow.wdl

@@ -1,46 +1,17 @@
 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
 
 workflow {{ project_name }} {
+	String sample_id	
 	File read1
 	File read2
-	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_docker
 	String fastp_cluster
+	String disk_size
 	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 
@@ -53,24 +24,27 @@ workflow {{ project_name }} {
 	Int qualified_quality_phred
 	Int length_required1
 	Int disable_quality_filtering
+
+	File idx
+	String idx_prefix
+	String pen_intronlen
+	String hisat2_docker
+	String hisat2_cluster
+	String samtools_docker
+	String samtools_cluster
+	Int trim_front1 
 	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
-	Float minimum_isoform_abundance
-	Float maximum_fraction_of_muliplelocationmapped_reads
-	String ballgown_docker
-	String ballgown_cluster
-	String disk_size
+	String samtools_docker
+	String samtools_cluster
+
 
 	call fastp.fastp as fastp {
 		input: 
@@ -98,26 +72,6 @@ workflow {{ project_name }} {
 		disable_quality_filtering = disable_quality_filtering
 		}
 
-	call fastqc.fastqc as fastqc {
-		input:
-		read1 = fastp.Trim_R1, 
-		read2 = fastp.Trim_R2,
-		docker = fastqc_docker,
-		cluster_config = fastqc_cluster_config,
-		disk_size = fastqc_disk_size
-	}
-
-	call fastqscreen.fastq_screen as fastqscreen {
-		input:
-		read1 = fastp.Trim_R1, 
-		read2 = fastp.Trim_R2,
-		screen_ref_dir = screen_ref_dir,
-		fastq_screen_conf = fastq_screen_conf,
-		docker = fastqscreen_docker,
-		cluster_config = fastqscreen_cluster_config,
-		disk_size = fastqscreen_disk_size
-	}
-
 	call hisat2.hisat2 as hisat2 {
 		input: 
 		sample_id = sample_id, 
@@ -146,45 +100,5 @@ workflow {{ project_name }} {
 		disk_size = disk_size,
 		insert_size = insert_size
 	}
-			
-	call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
-		input:
-		bam = samtools.out_percent,
-		docker = qualimapBAMqc_docker,
-		cluster_config = qualimapBAMqc_cluster_config,
-		disk_size = qualimapBAMqc_disk_size
-	}
 
-	call qualimapRNAseq.qualimapRNAseq as qualimapRNAseq {
-		input:
-		bam = samtools.out_percent,
-		docker = qualimapRNAseq_docker,
-		cluster_config = qualimapRNAseq_cluster_config,
-		disk_size = qualimapRNAseq_disk_size,
-		gtf = gtf
-	}
-
-	call stringtie.stringtie as stringtie {
-		input: 
-		sample_id = sample_id,
-		gtf = gtf, 
-		bam = samtools.out_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 ballgown.ballgown as ballgown {
-		input: 
-		sample_id = sample_id,
-		docker = ballgown_docker,
-		cluster = ballgown_cluster,
-		ballgown = stringtie.ballgown,
-		gene_abundance = stringtie.gene_abundance,
-		disk_size = disk_size
-	} 
 }