修改错误脚本

tasks/Dedup.wdl.bak

-task Dedup {
-
-	String sample
-
-	File unsorted_bam
-
-	String docker
-	String cluster_config
-	String disk_size
-
-
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		deduplicate_bismark -p --bam ${unsorted_bam}	
-	>>>
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File Dedup_bam = "${sample}_R1_val_1_bismark_bt2_pe.deduplicated.bam"
-	}
-}
-
-
-
-
-
-

tasks/Mapping.wdl.bak

-task mapping {
-
-    File ref_dir
-	File trim_read1
-	File trim_read2
-
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e	
-		nt=$(nproc)
-		bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
-
-	>>>
-
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File unsorted_bam = "${sample}_R1_val_1_bismark_bt2_pe.bam"
-	}
-}

tasks/Trim.wdl

 	command <<<
 		set -o pipefail
 		set -e
-		trim_galore --clip_R1 4 --clip_R2 4 --three_prime_clip_R1 4 --three_prime_clip_R2 4 --paired ${fastq1} ${fastq2}
-		
+		trim_galore --clip_R1 4 --clip_R2 4 --three_prime_clip_R1 4 --three_prime_clip_R2 4 --paired ${fastq_1} ${fastq_2}
 	>>>
 
 	runtime {