fixup

tasks/Call_meth.wdl

@@ -12,7 +12,7 @@ task Call_meth {
 command <<<
 		set -o pipefail
 		set -e
-		/src/Bismark-0.20.1/bismark_methylation_extractor --multicore 16 -p --no_overlap --comprehensive --report --bedGraph --cytosine_report -o ./ --gzip --ignore_r2 2 --genome_folder ${ref_dir} ${Dedup_bam}
+		/src/Bismark-0.20.1/bismark_methylation_extractor --multicore 4 -p --no_overlap --comprehensive --report --bedGraph --cytosine_report -o ./ --gzip --ignore_r2 2 --genome_folder ${ref_dir} ${Dedup_bam}
 		gunzip "${sample}.deduplicated.bedGraph.gz"
 		bedtools sort -i ${sample}.deduplicated.bedGraph > ${sample}.deduplicated.sorted.bedGraph
 		/usr/local/bin/bedGraphToBigWig ${sample}.deduplicated.sorted.bedGraph ${chrom_sizes_dir}/${chrom_sizes} ${sample}.deduplicated.bw

tasks/Mapping.wdl

@@ -12,7 +12,7 @@ task Mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		/src/Bismark-0.20.1/bismark --bowtie2 -p 8 --multicore 8 --bam ${ref_dir} -1 ${fastq_1} -2 ${fastq_2}
+		/src/Bismark-0.20.1/bismark --bowtie2 -p 16 --multicore 2 --bam ${ref_dir} -1 ${fastq_1} -2 ${fastq_2}
 
 	>>>