second 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.json

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

tasks/teprof_s2.wdl

+task teprof_s2 {
+    String sample_id
+    File bam_file
+    File filter_combined_candidates
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir filterreadstats
+        cp ${bam_file} ./
+        samtools index -b -@ 16 ${sample_id}.Aligned.sortedByCoord.out.bam
+        now_path=`pwd`
+        python /database/rnapipelinerefhg38/rnapipeline/commandsmax_speed.py ${filter_combined_candidates} $now_path/
+        grep ${sample_id} filterreadcommands.txt > ${sample_id}_filterreadcommands.txt
+        parallel -j 16 < ${sample_id}_filterreadcommands.txt
+        mv filterreadstats ${sample_id}_filterreadstats
+        tar -zcvf ${sample_id}_filterreadstats.tgz ${sample_id}_filterreadstats
+
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File filterreadcommands = "${sample_id}_filterreadcommands.txt"
+        File filterreadstats = "${sample_id}_filterreadstats.tgz"
+    }
+
+}
+

workflow.wdl

+import "./tasks/teprof_s2.wdl" as teprof_s2
+
+workflow {{ project_name }} {
+    String sample_id
+    File bam_file
+    File filter_combined_candidates
+    String disk_size
+
+
+    String teprof_docker
+    String teprof_cluster
+
+
+
+        call teprof_s2.teprof_s2 as teprof_s2 {
+                input:
+                sample_id=sample_id,
+                bam_file=bam_file,
+                filter_combined_candidates=filter_combined_candidates,
+                disk_size=disk_size,
+                docker=teprof_docker,
+                cluster=teprof_cluster
+        }
+
+
+
+}