rna-seq/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
	}

	# 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")
	}
}