first commit

README.md

@@ -0,0 +1,45 @@
+# README.md
+
+> Author: Qingwang Chen
+>
+> Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn)
+>
+> Last Updates: 05/11/2020
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+```
+# 激活choppy环境
+$ source activate choppy (open-choppy-env)
+
+# 第一次安装
+$ choppy install chenqingwang/featureCounts
+# 非第一次安装
+$ choppy install chenqingwang/featureCounts -f 
+
+# 查询已安装APP
+$ choppy apps
+```
+
+#### Quick Start
+
+```
+# 准备 samples.csv 文件
+$ choppy samples chenqingwang/featureCounts-latest > samples.csv
+
+# 提交任务
+$ choppy batch jchenqingwang/featureCounts-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

@@ -0,0 +1,6 @@
+{   
+	"lnc_gtf_file":"lncRNAKB_hg38_v7.gtf",
+	"gtf_dir":"oss://pgx-reference-data/reference/subread/",
+    "subread_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/subread:v1.6.4",
+    "subread_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    }

inputs

@@ -0,0 +1,8 @@
+{
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.bam_file": "{{ bam_file }}",
+	"{{ project_name }}.gtf_dir: "{{ gtf_dir }}",
+	"{{ project_name }}.lnc_gtf_file: "{{ lnc_gtf_file }}",
+	"{{ project_name }}.subread_docker": "{{ subread_docker }}",
+	"{{ project_name }}.subread_cluster": "{{ subread_cluster }}"
+}

tasks/featureCounts.wdl

@@ -0,0 +1,27 @@
+task featureCounts {
+    File bam_file
+    File lnc_gtf_file
+    String gtf_dir
+    String sample_id
+    String docker
+    String cluster
+
+
+    
+    command <<<
+        featureCounts -T 4 -t exon -g gene_id -a ${gtf_dir}/${lnc_gtf_file} -s 0 -p -o ${sample_id}.genefeaturecount.txt ${bam_file}
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd 200 /cromwell_root/"
+    }
+
+    output {
+        File out_profile = "${sample_id}.genefeaturecount.txt"
+        File out_summary = "${sample_id}.summary"
+    }
+}
+

workflow.wdl

@@ -0,0 +1,22 @@
+import "./tasks/fastp.wdl" as fastp
+import "./tasks/hisat2.wdl" as hisat2
+import "./tasks/samtools.wdl" as samtools
+import "./tasks/featureCounts.wdl" as featureCounts
+
+
+workflow {{ project_name }} {
+    String sample_id
+    File bam_file	
+    File lnc_gtf_file
+    String gtf_dir
+    String subread_docker
+    String subread_cluster	
+
+	call featureCounts.featureCounts as featureCounts {
+		input: 
+		sample_id = sample_id,
+		bam_file = bam_file, 
+		docker = subread_docker,
+		cluster = subread_cluster
+	}
+}