Added pigz instead of gzip

prepare_vm.sh

@@ -4,7 +4,7 @@ echo "#### Updating Ubuntu dist..."
 sudo apt update && sudo apt -y upgrade
 
 echo "#### Installing some Ubuntu packages..."
-sudo apt -y install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full
+sudo apt -y install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full pigz
 
 echo "#### Installing samtools 1.10..."
 cd ~

wgbs-pipeline.sh

@@ -307,21 +307,21 @@ fi
 
 echo -ne "     1.5 Extracting MT and Lambda methylation... "
 
-CMD="cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
+CMD="cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
     ${output_dir}/CpG_context_chrM_${sample_id}.dedup.txt.gz && \
-    cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
+    cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
     ${output_dir}/CpG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
-    gzip ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt \n\
-cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
+    pigz ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt \n\
+cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
     ${output_dir}/CHH_context_chrM_${sample_id}.dedup.txt.gz && \
-    cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
+    cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
     ${output_dir}/CHH_context_LAMBDA_${sample_id}.dedup.txt.gz && \
-    gzip ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt \n\
-cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
+    pigz ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt \n\
+cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
     ${output_dir}/CHG_context_chrM_${sample_id}.dedup.txt.gz && \
-    cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
+    cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
     ${output_dir}/CHG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
-    gzip ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt \n\
+    pigz ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt \n\
     zcat ${output_dir}/C??_context_LAMBDA_${sample_id}.dedup.txt.gz | python3 ${meth_prop} > \
     ${output_dir}/Lambda_meth_prop_${sample_id}.txt"
 echo -e ${CMD} > ${log_dir}/1_5_extract_MT.cmd