更新docker

tasks/Call_meth.wdl

@@ -11,7 +11,7 @@ task Call_meth {
 command <<<
 		set -o pipefail
 		set -e
-		bismark_methylation_extractor -p --no_overlap --comprehensive --report --bedGraph --genome_folder ${ref_dir} ${Dedup_bam}
+		/src/Bismark-0.20.1/bismark_methylation_extractor -p --no_overlap --comprehensive --report --bedGraph --genome_folder ${ref_dir} ${Dedup_bam}
 	>>>
 	
 	runtime {
@@ -30,5 +30,3 @@ command <<<
 		File CpG_context = "CpG_context_${sample}_R1_bismark_bt2_pe.txt"
 	}
 }
-
-

tasks/Dedup.wdl

@@ -9,9 +9,7 @@ task Dedup {
 	command <<<
 		set -o pipefail
 		set -e
-		cp ${unsorted_bam} ./
-		inputfile = basename ${unsorted_bam}
-		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ./$inputfile
+		/src/Bismark-0.20.1/deduplicate_bismark -p --bam ./$inputfile --output_dir ./
 	>>>
 	runtime {
 		docker:docker
@@ -21,8 +19,8 @@ task Dedup {
 	}
 
 	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 = "${sample}_R1_bismark_bt2_pe.deduplicated.bam"
+		File Dedup_repoet = "${sample}_R1_bismark_bt2_pe.deduplication_report.txt"
 	}
 }
 

tasks/Mapping.wdl

@@ -12,7 +12,7 @@ task Mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
+		/src/Bismark-0.20.1/bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
 
 	>>>
 

workflow.wdl

@@ -40,7 +40,7 @@ workflow {{ project_name }} {
 	call Call_meth.Call_meth as Call_meth {
 		input:
 		ref_dir=ref_dir,
-		Dedup_bam=Dedup.dedup_bam,
+		Dedup_bam=Dedup.Dedup_bam,
 		sample=sample,
 		docker=docker,
 		disk_size=disk_size,