first commit

README.md

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+# CNVkit
+
+> Author： Yaqing Liu
+>
+> E-mail：yaqing.liu@outlook.com
+>
+
+## 安装指南
+
+```
+# 激活choppy环境
+open-choppy-env
+# 安装app
+choppy install YaqingLiu/CNVkit
+```
+
+## Copy number calling pipeline
+![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)
+
+
+## App输入文件

defaults

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+{
+    "fasta": "GRCh38.d1.vd1.fa",
+    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+    "docker": "registry.cn-hangzhou.aliyuncs.com/pgx-docker-registry/cnvkit:0.9.7",
+    "disk_size": "200",
+    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+    "bed": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed"
+}

inputs

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+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.normal_bai": "{{ normal_bai }}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.tumor_bai": "{{ tumor_bai }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.bed": "{{ bed }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/access.wdl

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+task access {
+    File ref_dir
+    String fasta
+    String docker
+	String cluster_config
+	String disk_size
+
+    command <<<
+		cnvkit.py access ${ref_dir}/${fasta} -o ./data/access-5kb-mappable.hg38.bed
+    >>>
+   
+    runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File access_bed = "access-5kb-mappable.hg38.bed"
+    }
+}

tasks/batch.wdl

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+task batch {
+    String sample_id
+    File tumor_bam
+    File tumor_bai
+    File normal_bam
+    File normal_bai
+    String bed
+    File ref_dir
+    String fasta
+    File access_bed
+    String docker
+	String cluster_config
+	String disk_size
+
+    command <<<
+        cnvkit.py batch ${tumor_bam} --normal ${normal_bam} \
+        --targets ${bed} \
+        --fasta ${ref_dir}/${fasta} --access ${access_bed} \
+        --output-reference my_reference.cnn --output-dir ./results/ \
+        --diagram --scatter
+    >>>
+   
+    runtime { 
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File reference_cnn = "my_reference.cnn"
+        Array[File] result = glob("result/*")
+    }
+}
+
+
+

tasks/export.wdl

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+task export{
+    Array[File] result
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+		mkdir -p /cromwell_root/tmp/cnvkit_export
+		cp -r ${sep=" " result} /cromwell_root/tmp/cnvkit_export
+		cd /cromwell_root/tmp/cnvkit_export
+		# this version app just provides seg
+		cnvkit.py export seg ./results/*.cns -o samples.seg
+    >>>
+   
+    runtime { 
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File seg = "samples.seg"
+    }
+}

workflow.wdl

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+import "./tasks/access.wdl" as access
+import "./tasks/batch.wdl" as batch
+import "./tasks/export.wdl" as export
+
+workflow {{ project_name }} {	
+    String sample_id
+    File tumor_bam
+    File tumor_bai
+    File normal_bam
+    File normal_bai
+    String bed
+    File ref_dir
+    String fasta
+	String docker
+    String cluster
+    String disk_size
+
+	call access.access as access {
+		input: 
+		fasta=fasta,
+		ref_dir=ref_dir,
+		docker = docker,
+		cluster = cluster,
+		disk_size = disk_size
+	}
+
+	call batch.batch as batch {
+		input: 
+		sample_id = sample_id,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		tumor_bam = tumor_bam,
+		tumor_bai = tumor_bai,
+		normal_bam = normal_bam,
+		normal_bai = normal_bai,
+		bed = bed,
+		access_bed = access.access_bed,
+		docker = docker,
+		cluster = cluster,
+		disk_size = disk_size
+	}
+
+	call export.export as export {
+		input:
+		result = batch.result,
+		docker = docker,
+		cluster = cluster,
+		disk_size = disk_size
+	}
+}