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Gonzalo S Nido
wgbs-pipeline
Commits
5d46a9f4
Commit
5d46a9f4
authored
Aug 25, 2020
by
Gonzalo S Nido
Browse files
Quick fix
parent
22296bd9
Changes
1
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wgbs-pipeline.sh
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5d46a9f4
...
...
@@ -61,8 +61,6 @@ if ! grep -m1 -q "^>${LAMBDA_chr_name}" ${b38_ref}/Bisulfite_Genome/CT_conversio
exit
1
fi
exit
2
# Exit when any command fails
set
-e
...
...
@@ -306,6 +304,7 @@ else
echo
"DONE"
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 >
\
...
...
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