rna-seq-tophat/tasks/fastqc.wdl

task qc {
	File read
	String docker
	String cluster
	String out_dir = "./"

	command {
		fastqc -o ${out_dir} ${read}
	}

	runtime {
		docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd 200 /cromwell_root/"
	}

	# 输入文件后缀必须为.fq.gz或者.fastq.gz
	output {
		File html = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
		File zip = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
	}
}