Commit d12c7475 authored by Laura Denies's avatar Laura Denies
Browse files

Update Phage.smk: update empty file failsafe

parent 6a383de0
...@@ -38,11 +38,11 @@ rule aggregate_VirSorter: ...@@ -38,11 +38,11 @@ rule aggregate_VirSorter:
message: "VirSorter failsave for empty files: {wildcards.project} - {wildcards.sample}" message: "VirSorter failsave for empty files: {wildcards.project} - {wildcards.sample}"
shell: shell:
""" """
if [ -s {output} ] if [ -s {input} ]
then then
cp scripts/virsorter_headers.csv {output}
else
mv {input} {output} mv {input} {output}
else
cp scripts/virsorter_headers.csv {output}
fi fi
rm -rf {config[pathofact][datadir]}/{wildcards.project}/PathoFact_intermediate/MGE/phage/{wildcards.sample}/virsorter rm -rf {config[pathofact][datadir]}/{wildcards.project}/PathoFact_intermediate/MGE/phage/{wildcards.sample}/virsorter
""" """
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment