add-disk-size

inputs

@@ -5,6 +5,7 @@
     "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
     "{{ project_name }}.idx": "{{ idx }}",
     "{{ project_name }}.gtf": "{{ gtf }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}",
     "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
     "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
     "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",

workflow.wdl

@@ -12,6 +12,7 @@ workflow {{ project_name }} {
     File idx
 	String idx_prefix
     File gtf
+	String disk_size
     String fastqc_docker
     String fastqc_cluster
 	String fastqscreen_docker
@@ -31,7 +32,8 @@ workflow {{ project_name }} {
 		read1=read1,
 		read2=read2,
 		docker = fastqc_docker,
-		cluster = fastqc_cluster
+		cluster = fastqc_cluster,
+		disk_size= disk_size
 		}
 			
 	call fastqscreen.fastqscreen as fastqscreen {
@@ -41,7 +43,8 @@ workflow {{ project_name }} {
 		docker = fastqscreen_docker,
 		cluster = fastqscreen_cluster,
 		screen_ref_dir=screen_ref_dir,
-		fastq_screen_conf=fastq_screen_conf
+		fastq_screen_conf=fastq_screen_conf,
+		disk_size= disk_size
 		}	
 	
 	call hisat2.hisat2 as hisat2 {
@@ -51,14 +54,16 @@ workflow {{ project_name }} {
 		idx=idx, 
 		idx_prefix=idx_prefix, 
 		read_1P=read1, 
-		read_2P=read2
+		read_2P=read2,
+		disk_size= disk_size
 	}
 
     call samtools.samtools as samtools {
         input: 
 		docker = samtools_docker,
 		cluster = samtools_cluster,
-		sam = hisat2.sam
+		sam = hisat2.sam,
+		disk_size= disk_size
 	}
 
     call stringtie.stringtie as stringtie {
@@ -66,7 +71,8 @@ workflow {{ project_name }} {
 		docker = stringtie_docker,
 		cluster = stringtie_cluster,
 		gtf = gtf, 
-		bam = samtools.out_bam
+		bam = samtools.out_bam,
+		disk_size= disk_size
 	}   
 
 	call ballgown.ballgown as ballgown {
@@ -74,7 +80,8 @@ workflow {{ project_name }} {
 		docker = ballgown_docker,
 		cluster = ballgown_cluster,
 		ballgown = stringtie.ballgown,
-		gene_abundance = stringtie.gene_abundance
+		gene_abundance = stringtie.gene_abundance,
+		disk_size= disk_size
 	} 
 	
 }