Commit 5d46a9f4 authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Quick fix

parent 22296bd9
...@@ -61,8 +61,6 @@ if ! grep -m1 -q "^>${LAMBDA_chr_name}" ${b38_ref}/Bisulfite_Genome/CT_conversio ...@@ -61,8 +61,6 @@ if ! grep -m1 -q "^>${LAMBDA_chr_name}" ${b38_ref}/Bisulfite_Genome/CT_conversio
exit 1 exit 1
fi fi
exit 2
# Exit when any command fails # Exit when any command fails
set -e set -e
...@@ -306,6 +304,7 @@ else ...@@ -306,6 +304,7 @@ else
echo "DONE" echo "DONE"
fi fi
echo -ne " 1.5 Extracting MT and Lambda methylation... " 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} | gzip -nc > \
......
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