删除 'tasks/fastqscreen.wdl'

tasks/fastqscreen.wdl

@@ -1,37 +0,0 @@
-task fastq_screen {
-	File read1
-	File read2
-	File screen_ref_dir
-	File fastq_screen_conf
-	String read1name = basename(read1,".fastq.gz")
-	String read2name = basename(read2,".fastq.gz")
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${screen_ref_dir} /cromwell_root/tmp/
-		#sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
-	>>>
-
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File png1 = "${read1name}_screen.png"
-		File txt1 = "${read1name}_screen.txt"
-		File html1 = "${read1name}_screen.html"
-		File png2 = "${read2name}_screen.png"
-		File txt2 = "${read2name}_screen.txt"
-		File html2 = "${read2name}_screen.html"
-	}
-}