first commit

inputs

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+{
+    "{{ project_name }}.read1": "{{ read1 }}",
+    "{{ project_name }}.read2": "{{ read2 }}",
+    "{{ project_name }}.baseout": "{{ baseout }}",
+    "{{ project_name }}.adapter": "oss://pgx-reference-data/reference/illumina_adapter/",
+    "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.38",
+    "{{ project_name }}.cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
+    "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/trimmomatic.wdl

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+task trimmomatic {
+	File read1
+	File read2
+	File adapter
+	String baseout
+    String baseout_gz = baseout + ".fq.gz"
+	String docker
+	String cluster
+	String disk_size
+
+	command <<<
+			nt=$(nproc)
+           /opt/conda/bin/trimmomatic PE -threads $nt -phred33 ${read1} ${read2} -baseout ${baseout_gz} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
+        >>>
+
+		runtime {
+			docker: docker
+			cluster: cluster
+			systemDisk: "cloud_ssd 40"
+			dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+        output {
+           File read_1p = baseout + "_1P.fq.gz"
+           File read_2p = baseout + "_2P.fq.gz"
+	}
+}

workflow.wdl

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+import "./tasks/trimmomatic.wdl" as trimmomatic
+
+workflow {{ project_name }} {
+
+	File read1
+	File read2
+	File adapter
+	String baseout
+	String docker
+	String cluster
+	String disk_size
+	
+	
+	call trimmomatic.trimmomatic as trimmomatic {
+		input: 
+			read1=read1, 
+			read2=read2, 
+			adapter= adapter,
+			baseout=baseout,
+			docker=docker,
+			cluster=cluster,
+			disk_size=disk_size
+	}
+	
+}
+
+
+