add cat

inputs

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+{
+  "{{ project_name }}.raw_name": "{{ raw_name }}",
+  "{{ project_name }}.new_name": "{{ new_name }}"
+}

tasks/cat_rename.wdl

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+task bamqc {
+	String raw_name
+	String new_name
+	String cluster_config
+
+	command <<<
+		cat ${raw_name}/clean/*_1.fq.gz > ${new_name}_1.fq.gz
+		cat ${raw_name}/clean/*_2.fq.gz > ${new_name}_2.fq.gz
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		new_name_fq_1 = "${new_name}_1.fq.gz"
+		new_name_fq_2 = "${new_name}_2.fq.gz"
+	}
+}

workflow.wdl

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+import "./tasks/cat_rename.wdl" as cat_rename
+
+workflow {{ project_name }} {
+	String docker
+	String cluster_config
+	String disk_size
+	String raw_name
+	String new_name
+
+	call cat_rename.cat_rename as cat_rename {
+		input:
+			raw_name=raw_name,
+			docker=docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+	}
+}