add qualimap

defaults

     "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
     "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+    "qualimap_cluster": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
     "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
     "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
     "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",

inputs

     "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
     "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
     "{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
+    "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
+    "{{ project_name }}.qualimap_cluster": "{{ qualimap_cluster }}",
     "{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
     "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
     "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",

tasks/qualimap.wdl

+task qualimap {
+	File bam
+	File bai
+	File gtf
+	String bamname = basename(bam,".bam")
+	String docker
+	String cluster
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=10G
+		tar -zcvf ${bamname}_RNAseq_qualimap.zip ${bamname}_rnaseq
+        /opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File rnaseq_zip = "${bamname}_RNAseq_qualimap.zip"
+        File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
+	}
+}

workflow.wdl

 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
+import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/hisat2.wdl" as hisat2
 import "./tasks/samtools.wdl" as samtools
 import "./tasks/stringtie.wdl" as stringtie
 		disk_size= disk_size
 	}
 
+	call qualimap.qualimap as qualimap {
+		input:
+		bam = samtools.out_bam,
+		bai = samtools.out_bam_index,
+		gtf = gtf, 
+		docker = qualimap_docker,
+		cluster = qualimap_cluster,
+		disk_size = disk_size
+		}
+
     call stringtie.stringtie as stringtie {
         input: 
 		docker = stringtie_docker,