add-ballgown-task

inputs

@@ -44,22 +44,18 @@
 	"{{ project_name }}.maximum_fraction_of_muliplelocationmapped_reads": "{{ maximum_fraction_of_muliplelocationmapped_reads }}",
 	"{{ project_name }}.fastqc_cluster_config": "{{ fastqc_cluster_config }}",
 	"{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
-	"{{ project_name }}.fastqc_disk_size": "{{ fastqc_disk_size }}",
 	"{{ project_name }}.qualimapBAMqc_docker": "{{ qualimapBAMqc_docker }}",
 	"{{ project_name }}.qualimapBAMqc_cluster_config": "{{ qualimapBAMqc_cluster_config }}",
-	"{{ project_name }}.qualimapBAMqc_disk_size": "{{ qualimapBAMqc_disk_size }}",
 	"{{ project_name }}.qualimapRNAseq_docker": "{{ qualimapRNAseq_docker }}",
 	"{{ project_name }}.qualimapRNAseq_cluster_config": "{{ qualimapRNAseq_cluster_config }}",
-	"{{ project_name }}.qualimapRNAseq_disk_size": "{{ qualimapRNAseq_disk_size }}",
 	"{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
 	"{{ project_name }}.fastqscreen_cluster_config": "{{ fastqscreen_cluster_config }}",
 	"{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
 	"{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
-	"{{ project_name }}.fastqscreen_disk_size": "{{ fastqscreen_disk_size }}",
 	"{{ project_name }}.ref_dir": "{{ ref_dir }}",
 	"{{ project_name }}.multiqc_cluster_config": "{{ multiqc_cluster_config }}",
 	"{{ project_name }}.multiqc_docker": "{{ multiqc_docker }}",
-	"{{ project_name }}.multiqc_disk_size": "{{ multiqc_disk_size }}",
 	"{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
 	"{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}"
+	"{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
 }

tasks/ballgown.wdl

@@ -1,15 +1,14 @@
 task ballgown {
     File gene_abundance
-    String base = basename(gene_abundance, ".gene.abundance.txt")
     Array[File] ballgown
     String docker
     String cluster
     String disk_size
 
     command <<<
-      mkdir -p /cromwell_root/tmp/${base}
-      cp -r ${sep=" " ballgown} /cromwell_root/tmp/${base}
-      ballgown /cromwell_root/tmp/${base} ${base}.txt
+      mkdir -p /cromwell_root/tmp/${sample_id}
+      cp -r ${sep=" " ballgown} /cromwell_root/tmp/${sample_id}
+      ballgown /cromwell_root/tmp/${sample_id} ${sample_id}.txt
     >>>
     
     runtime {
@@ -20,6 +19,6 @@ task ballgown {
     }
     
     output {
-      File mat_expression = "${base}.txt"
+      File mat_expression = "${sample_id}.txt"
     }
 }

tasks/fastqc.wdl

@@ -1,8 +1,6 @@
 task fastqc {
 	File read1
 	File read2
-	String bamname1 = basename(read1,"\\.(fastq|fq)\\.gz$")
-	String bamname2 = basename(read2,"\\.(fastq|fq)\\.gz$")
 	String docker
 	String cluster_config
 	String disk_size

tasks/hisat2.wdl

@@ -23,7 +23,7 @@ task hisat2 {
 		docker: docker 
 		cluster: cluster
 		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd 200 /cromwell_root/"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
 
    output {

tasks/samtools.wdl

@@ -24,7 +24,7 @@ task samtools {
        docker: docker
        cluster: cluster
        systemDisk: "cloud_ssd 40"
-       dataDisk: "cloud_ssd 200 /cromwell_root/"
+       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
     }
 
     output {

tasks/stringtie.wdl

@@ -20,7 +20,7 @@ task stringtie {
       docker: docker
       cluster: cluster
       systemDisk: "cloud_ssd 40"
-      dataDisk: "cloud_ssd 150 /cromwell_root/"
+      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
     }
     
     output {

workflow.wdl

@@ -172,4 +172,13 @@ workflow {{ project_name }} {
 		minimum_isoform_abundance = minimum_isoform_abundance,
 		maximum_fraction_of_muliplelocationmapped_reads = maximum_fraction_of_muliplelocationmapped_reads
 		}
+
+		call ballgown.ballgown as ballgown {
+		input: 
+		docker = ballgown_docker,
+		cluster = ballgown_cluster,
+		ballgown = stringtie.ballgown,
+		gene_abundance = stringtie.gene_abundance,
+		disk_size = disk_size
+		} 
 }