first commit

defaults

+{   
+    "teprof_docker":"registry.cn-shanghai.aliyuncs.com/shaolab_docker/teprof:1.5",
+    "teprof_cluster":"OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+    "disk_size":"300"
+}

inputs

+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.bam_file": "{{ bam_file }}",
+    "{{ project_name }}.reference_merged_candidates_gtf": "{{ reference_merged_candidates_gtf }}",
+    "{{ project_name }}.teprof_docker": "{{ teprof_docker }}",
+    "{{ project_name }}.teprof_cluster": "{{ teprof_cluster }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/teprof_s3.wdl

+task teprof_s3 {
+    String sample_id
+    File bam_file
+    File reference_merged_candidates_gtf
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+        samtools view -@ 16 -q 255 -h ${bam_file} > ${sample_id}.filtered.Aligned.sortedByCoord.out.bam
+        stringtie ${sample_id}.filtered.Aligned.sortedByCoord.out.bam -o ${sample_id}.Aligned.sortedByCoord.out_root.gtf -e -b ${sample_id}.Aligned.sortedByCoord.out_root_stats -p 16 -m 100 -c 1 -G ${reference_merged_candidates_gtf} --rf
+        tar -zcvf ${sample_id}.Aligned.sortedByCoord.out_root_stats.tgz ${sample_id}.Aligned.sortedByCoord.out_root_stats
+        rm ${sample_id}.filtered.Aligned.sortedByCoord.out.bam
+
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File stringtie_stats = "${sample_id}.Aligned.sortedByCoord.out_root_stats.tgz"
+        File stringtie_gtf = "${sample_id}.Aligned.sortedByCoord.out_root.gtf"
+    }
+
+}
+

workflow.wdl

+import "./tasks/teprof_s3.wdl" as teprof_s3
+
+workflow {{ project_name }} {
+    String sample_id
+    File bam_file
+    File reference_merged_candidates_gtf
+    String disk_size
+
+
+    String teprof_docker
+    String teprof_cluster
+
+
+
+        call teprof_s3.teprof_s3 as teprof_s3 {
+                input:
+                sample_id=sample_id,
+                bam_file=bam_file,
+                reference_merged_candidates_gtf=reference_merged_candidates_gtf,
+                disk_size=disk_size,
+                docker=teprof_docker,
+                cluster=teprof_cluster
+        }
+
+}