first commit

inputs

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+{
+  "{{ project_name }}.fq1": "{{ fq1 }}",
+  "{{ project_name }}.fq2": "{{ fq2 }}",
+  "{{ project_name }}.fq_m": "{{ fq_m }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
+}

sample.csv

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+sample_id,fq1,fq2,disk_size,fq_m
+mergefq,oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R1_400k.gz,oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R2_400k.gz,10,Quartet_RNA_ILM_NovaSeq.fastq.gz

tasks/mergefq.wdl

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+task mergefq {
+	File fq1
+	File fq2
+	String fq_m
+	String disk_size
+	String docker
+	String cluster_config
+
+	command <<<
+		set -euo pipefail
+		cat ${fq1} ${fq2} > ${fq_m}
+	>>>
+
+	runtime {
+		docker: docker
+		systemDisk: "cloud_ssd 40"
+		cluster: cluster_config
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File merge_fq = "${fq_m}"
+	}
+}

workflow.wdl

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+import "./tasks/mergefq.wdl" as mergefq
+
+workflow {{ project_name }} {
+	File fq1
+	File fq2
+	String fq_m
+	String disk_size
+	String docker
+	String cluster_config
+
+	call mergefq.mergefq as mergefq {
+		input:
+			fq1=fq1,
+			fq2=fq2,
+			fq_m=fq_m,
+			docker=docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+	}
+}