Commit 7ef42c14 authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Added -f to pigz

parent c61a9725
......@@ -439,17 +439,17 @@ if [[ $S1 == "true" ]]; then
${output_dir}/CpG_context_chrM_${sample_id}.dedup.txt.gz && \
cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
${output_dir}/CpG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
pigz ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt \n\
pigz -f ${output_dir}/CpG_context_b38_${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} | pigz -nc > \
${output_dir}/CHH_context_LAMBDA_${sample_id}.dedup.txt.gz && \
pigz ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt \n\
pigz -f ${output_dir}/CHH_context_b38_${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} | pigz -nc > \
${output_dir}/CHG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
pigz ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt \n\
pigz -f ${output_dir}/CHG_context_b38_${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
......
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