first commit

README.md

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+### NGSCheckMate - vaf_ncm
+
+### Getting Started
+
+We recommend using choppy system and Aliyun OSS service. The command will look like this:
+
+```
+# Activate the choppy environment
+$ open-choppy-env
+
+# Install the APP
+$ choppy install YaqingLiu/vaf_ncm-latest [-f]
+
+# List the parameters
+$ choppy samples YaqingLiu/vaf_ncm-latest [--no-default]
+
+# Submit you task with the `samples.json file` and `project name`
+$ choppy batch YaqingLiu/vaf_ncm-latest samples.json -p Project [-l project:Label]
+
+# Query the status of all tasks in the project
+$ choppy query -L project:Label | grep "status"
+```

defaults

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+{
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "disk_size": "100",
+  "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/ngscheckmate:v1.0.0"
+}

inputs

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+{
+  "{{ project_name }}.vaf": {{ vaf | tojson }},
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/vaf_ncm.wdl

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+task vaf_ncm {
+  
+  Array[File] vaf
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    export NCM_HOME=/opt/NGSCheckMate
+
+    mkdir -p /ncm/fastq_vaf/
+    cp ${sep=" " vaf} /ncm/fastq_vaf/
+
+    python /opt/NGSCheckMate/vaf_ncm.py -I /ncm/fastq_vaf/ -O '.' -f -p $nt
+  >>>
+
+  runtime {
+    docker:docker
+      cluster:cluster_config
+      systemDisk:"cloud_ssd 40"
+      dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File all_txt="output_all.txt"
+    File cor_txt="output_corr_matrix.txt"
+    File r_script="r_script.r"
+    File Rout_script="r_script.r.Rout"
+  }
+}

workflow.wdl

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+import "./tasks/vaf_ncm.wdl" as vaf_ncm
+
+workflow {{ project_name }} {
+  
+  Array[File] vaf
+  String docker
+  String cluster_config
+  String disk_size
+
+  call vaf_ncm.vaf_ncm as vaf_ncm {
+    input:
+    vaf=vaf,
+    docker=docker,
+    disk_size=disk_size,
+    cluster_config=cluster_config
+  }
+}