first commit

README.md

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+### NGSCheckMate - ngscheckmate_fastq
+A C program, ngscheckmate_fastq, can be directly called to generate a VAF file from one FASTQ file (single-end sequencing) or two FASTQ files(paired-end sequencing). 
+
+### 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/ngscheckmate_fastq-latest [-f]
+
+# List the parameters
+$ choppy samples YaqingLiu/ngscheckmate_fastq-latest [--no-default]
+
+# Submit you task with the `samples.json file` and `project name`
+$ choppy batch YaqingLiu/ngscheckmate_fastq-latest samples.json -p Project [-l project:Label]
+
+# Query the status of all tasks in the project
+$ choppy query -L project:Label | grep "status"
+```
+
+#### other parameters
+- subsampling_rate: The default subsampling rate is 1. The speed is not very slow.

defaults

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+{
+  "subsampling_rate": "1",
+  "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 }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.fastq1": "{{ fastq1 }}",
+  "{{ project_name }}.fastq2": "{{ fastq2 }}",
+  "{{ project_name }}.output_id": "{{ output_id }}",
+  "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/fastq_ncm.wdl

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+task fastq_ncm {
+  
+  File fq1
+  File fq2
+  String out_id
+  String subsampling_rate
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    export NCM_HOME=/opt/NGSCheckMate
+    /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${out_id}.vaf
+  >>>
+
+  runtime {
+    docker:docker
+      cluster:cluster_config
+      systemDisk:"cloud_ssd 40"
+      dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File vaf="${out_id}.vaf"
+  }
+}

workflow.wdl

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+import "./tasks/fastq_ncm.wdl" as fastq_ncm
+import "./tasks/vaf_ncm.wdl" as vaf_ncm
+
+workflow {{ project_name }} {
+  
+  String sample_id
+  File fastq1
+  File fastq2
+  String output_id
+  String subsampling_rate
+  String docker
+  String cluster_config
+  String disk_size
+
+  call fastq_ncm.fastq_ncm as fastq_ncm {
+    input:
+    fq1=fastq1,
+    fq2=fastq2,
+    out_id=output_id,
+    subsampling_rate=subsampling_rate,
+    docker=docker,
+    disk_size=disk_size,
+    cluster_config=cluster_config
+  }
+}