first commit

README.md

+# Extract BAM for IGV
+
+> Author： Ren Luyao
+>
+> E-mail：18110700050@fudan.edu.cn
+>
+> Git: http://choppy.3steps.cn/renluyao/IGV_get_bam.git
+>
+> Last Updates: 2020/0705
+
+## 安装指南
+
+```
+# 激活choppy环境
+source activate choppy
+# 安装app
+choppy install renluyao/IGV_get_bam
+```
+
+## App概述
+
+为了IGV验证突变，截取其中一段bam文件
+
+## 流程与参数
+
+```bash
+samtools view -b ${bam} "${region}" > ${region}.${sample}.bam
+samtools index ${region}.${sample}.bam
+```
+
+samples文件中的region格式如下：
+
+```bash
+#chromo:start-end
+chr6:73900000-73920000
+```
+
+## App输出文件
+
+输出结果为截取的bam文件和相应的bam索引文件

inputs

+{
+  "{{ project_name }}.bam_idx": "{{ bam_idx }}",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.bed": {{ bed }},
+  "{{ project_name }}.sample": "{{ sample }}"
+}

tasks/getBam.wdl

+task getBam {
+	File bam
+	File bam_idx
+	String sample
+	File bed
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+			/opt/conda/bin/samtools view -bS -L ${bed} ${bam} > ${sample}.bam
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File sub_bam = "${sample}.bam"
+	}
+}
+

workflow.wdl

+import "./tasks/getBam.wdl" as getBam
+
+
+workflow {{ project_name }} {
+	
+	File bam
+	File bam_idx
+	File bed
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	call getBam.getBam as getBam {
+		input:	
+		bam=bam,
+		bam_idx=bam_idx,
+		sample=sample,
+		bed=bed,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+}
+