update_for_notrim

tasks/Call_meth.wdl

 command <<<
 		set -o pipefail
 		set -e
-		/src/Bismark-0.20.1/bismark_methylation_extractor -p --no_overlap --comprehensive --report --bedGraph --genome_folder ${ref_dir} ${Dedup_bam}
+		/src/Bismark-0.20.1/bismark_methylation_extractor --multicore 16 -p --no_overlap --comprehensive --report --bedGraph --cytosine_report --CX_context --ignore_r2 2 --merge_non_CpG --genome_folder ${ref_dir} ${Dedup_bam}
 	>>>
 	
 	runtime {
 		docker:docker
     	cluster: cluster_config
-    	systemDisk: "cloud_ssd 400"
+    	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 
 	output {
-		File bedGraph = "${sample}_R1_bismark_bt2_pe.deduplicated.bedGraph.gz"
-		File cov = "${sample}_R1_bismark_bt2_pe.bismark.deduplicated.cov.gz"
-		File splitting_report = "${sample}_R1_bismark_bt2_pe_splitting_report.deduplicated.txt"
-		File CHG_context = "CHG_context_${sample}_R1_bismark_bt2_pe.deduplicated.txt"
-		File CHH_context = "CHH_context_${sample}_R1_bismark_bt2_pe.deduplicated.txt"
-		File CpG_context = "CpG_context_${sample}_R1_bismark_bt2_pe.deduplicated.txt"
-		File Mbias = "${sample}_R1_bismark_bt2_pe.deduplicated.M-bias.txt"
+		File bedGraph = "${sample}.deduplicated.bedGraph.gz"
+		File cov = "${sample}.bismark.deduplicated.cov.gz"
+		File splitting_report = "${sample}.deduplicated_splitting_report.txt"
+		File CHG_context = "CHG_context_${sample}.deduplicated.txt"
+		File CHH_context = "CHH_context_${sample}.deduplicated.txt"
+		File CpG_context = "CpG_context_${sample}.deduplicated.txt"
+		File Mbias = "${sample}.deduplicated.M-bias.txt"
+		File CX = "${sample}.CX_report.txt"
 	}
 }

tasks/Dedup.wdl

 	}
 
 	output {
-		File Dedup_bam = "${sample}_R1_bismark_bt2_pe.deduplicated.bam"
-		File Dedup_repoet = "${sample}_R1_bismark_bt2_pe.deduplication_report.txt"
+		File Dedup_bam = "${sample}.deduplicated.bam"
+		File Dedup_repoet = "${sample}.deduplication_report.txt"
 	}
 }
 

tasks/Mapping.wdl

 	command <<<
 		set -o pipefail
 		set -e	
-		/src/Bismark-0.20.1/bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${fastq_1} -2 ${fastq_2}
+		/src/Bismark-0.20.1/bismark -B ${sample} --bowtie2 -p 16 --multicore 16 --bam ${ref_dir} -1 ${fastq_1} -2 ${fastq_2}
 
 	>>>
 
 	runtime {
 		docker:docker
     	cluster: cluster_config
-    	systemDisk: "cloud_ssd 500"
+    	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File bam = "${sample}_R1_bismark_bt2_pe.bam"
+		File bam = "${sample}.bam"
 	}
 }