add count and pre qc control

defaults

     "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",
-    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
+    "count_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "count_length": "150"
 }

inputs

     "{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
     "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
     "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
-    "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}"
+    "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
+    "{{ project_name }}.count_docker": "{{ count_docker }}",
+	"{{ project_name }}.count_cluster": "{{ count_cluster }}",
+	"{{ project_name }}.count_length": "{{ count_length }}",
+    "{{ project_name }}.pre_alignment_qc": "{{ pre_alignment_qc }}"
 }

tasks/count.wdl

+task count {
+    Array[File] ballgown
+    String sample_id
+    String docker
+    String cluster
+    String disk_size
+    Int count_length
+
+    command <<<
+      mkdir -p /cromwell_root/tmp/ballgown/${sample_id}
+      cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown/${sample_id}
+      count -i /cromwell_root/tmp/ballgown -l ${count_length} -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
+    >>>
+    
+    runtime {
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+    
+    output {
+      File mat_expression_genecount = "${sample_id}_gene_count_matrix.csv"
+      File mat_expression_transcriptcount = "${sample_id}_transcript_count_matrix.csv"
+    }
+}

workflow.wdl

 import "./tasks/samtools.wdl" as samtools
 import "./tasks/stringtie.wdl" as stringtie
 import "./tasks/ballgown.wdl" as ballgown
+import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
 
 	String ballgown_docker
 	String ballgown_cluster
 	
-	
-	call fastqc.fastqc as fastqc {
+	if (pre_alignment_qc) {
+		
+		call fastqc.fastqc as fastqc {
 		input:
 		read1=read1,
 		read2=read2,
 		cluster = fastqc_cluster,
 		disk_size = disk_size
 		}
-			
-	call fastqscreen.fastqscreen as fastqscreen {
+		
+		call fastqscreen.fastqscreen as fastqscreen {
 		input:
 		read1 = read1,
 		read2 = read2,
 		fastq_screen_conf = fastq_screen_conf,
 		disk_size = disk_size
 		}	
+	}
+	
 	
 	call hisat2.hisat2 as hisat2 {
 		input: 
 		gene_abundance = stringtie.gene_abundance,
 		disk_size = disk_size
 		} 
+	
+	call count.count as count {
+		input: 
+		sample_id = sample_id,
+		docker = count_docker,
+		cluster = count_cluster,
+		ballgown = stringtie.ballgown,
+		disk_size = disk_size,
+		count_length = count_length
+	}
 }