first commit

README.md

+# README.md
+
+> Author: Qingwang Chen
+>
+> Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn)
+>
+> Last Updates: 25/03/2021
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+```
+# 激活choppy环境
+$ source activate choppy (open-choppy-env)
+
+# 第一次安装
+$ choppy install chenqingwang/rMATS
+# 非第一次安装
+$ choppy install chenqingwang/rMATS -f 
+
+# 查询已安装APP
+$ choppy apps
+```
+
+#### Quick Start
+
+```
+# 准备 samples.csv 文件
+$ choppy samples chenqingwang/rMATS-latest > samples.csv
+# 准备无默认参数的samples.csv 文件
+choppy samples --no-default chenqingwang/rMATS-latest > samples.csv
+
+# 提交任务
+$ choppy batch chenqingwang/rMATS-latest samples.csv -p Your_project_name -l Your_label
+
+# 查询任务运行状况
+$ choppy query -L Your_label | grep "status"
+
+# 查询失败任务
+$ choppy search -s Failed -p Your_project_name -u chenqingwang --short-format
+
+# 结果文件地址
+$ oss://choppy-cromwell-result/test-choppy/Your_project_name/
+```

defaults

+{   
+    "reference_gtf_file":"oss://pgx-reference-data/reference/rmats/Homo_sapiens.GRCh38.103.gtf",
+    "rmats_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/rmats:4.1.1",
+    "rmats_cluster":"OnDemand bcs.a2.large img-ubuntu-vpc"，
+    "disk_size":"200"
+    }

inputs

+{
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.b1_txt": "{{ b1_txt }}",
+	"{{ project_name }}.b2_txt": "{{ b2_txt }}",
+	"{{ project_name }}.reference_gtf_file": "{{ reference_gtf_file }}",
+	"{{ project_name }}.rmats_docker": "{{ rmats_docker }}",
+	"{{ project_name }}.rmats_cluster": "{{ rmats_cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/rmats.wdl

+task rmats {
+    String sample_id
+    File b1_txt
+    File b2_txt
+    File reference_gtf_file
+    
+
+    String docker
+    String cluster
+    String disk_size
+
+
+    
+    command <<<
+        set -o pipefail
+        set -e
+
+        mkdir -p ${sample_id}
+        python /usr/local/bin/rmats.py --b1 ${b1_txt} \
+            --b2 ${b2_txt} \
+            --gtf ${reference_gtf_file} \
+            -t paired \
+            --readLength 150 \
+            --nthread 4 \
+            --od ${sample_id}/output \
+            --tmp ${sample_id}/tmp_output
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] AS_txt = glob("${sample_id}/output/*.txt")
+        Array[File] tmp = glob("${sample_id}/output/tmp/*")
+    }
+}
+

workflow.wdl

+import "./tasks/rmats.wdl" as rmats
+
+
+workflow {{ project_name }} {
+    String sample_id
+	File b1_txt
+    File b2_txt
+    File reference_gtf_file
+    
+
+    String rmats_docker
+    String rmats_cluster
+	String disk_size	
+
+	call rmats.rmats as rmats {
+		input:
+		b1_txt = b1_txt,
+		b2_txt = b2_txt,
+		reference_gtf_file = reference_gtf_file,
+		sample_id = sample_id,
+		bam_file = bam_file,
+		docker = rmats_docker,
+		cluster = rmats_cluster,
+		disk_size = disk_size
+	}
+}