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Laura Denies
PathoFact
Commits
d12c7475
Commit
d12c7475
authored
Sep 06, 2021
by
Laura Denies
Browse files
Update Phage.smk: update empty file failsafe
parent
6a383de0
Changes
1
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rules/AMR/Phage.smk
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d12c7475
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@@ -38,11 +38,11 @@ rule aggregate_VirSorter:
message: "VirSorter failsave for empty files: {wildcards.project} - {wildcards.sample}"
shell:
"""
if [ -s {
out
put} ]
if [ -s {
in
put} ]
then
cp scripts/virsorter_headers.csv
{output}
mv {input}
{output}
else
mv {input}
{output}
cp scripts/virsorter_headers.csv
{output}
fi
rm -rf {config[pathofact][datadir]}/{wildcards.project}/PathoFact_intermediate/MGE/phage/{wildcards.sample}/virsorter
"""
...
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