Commit 96415bbc authored by Laura Denies's avatar Laura Denies
Browse files

incorporated failsafe for empty VIRSorter prediction files

parent c0f66042
...@@ -38,7 +38,14 @@ rule aggregate_VirSorter: ...@@ -38,7 +38,14 @@ rule aggregate_VirSorter:
params: params:
outdir="{datadir}" outdir="{datadir}"
shell: shell:
"mv {input} {output}" """
if [ -s {output} ]
then
mv {input} {output}
else
cp scripts/virsorter_headers.csv {output}
fi
"""
# VIRFINDER Prediction # VIRFINDER Prediction
rule run_VirFinder: rule run_VirFinder:
......
## 1 - Complete phage contigs - category 1 (sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
## 2 - Complete phage contigs - category 2 (somewhat sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
## 3 - Complete phage contigs - category 3 (not so sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
## 4 - Prophages - category 1 (sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
## 5 - Prophages - category 2 (somewhat sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
## 6 - Prophages - category 3 (not so sure)
## Contig_id,Nb genes contigs,Fragment,Nb genes,Category,Nb phage hallmark genes,Phage gene enrichment sig,Non-Caudovirales phage gene enrichment sig,Pfam depletion sig,Uncharacterized enrichment sig,Strand switch depletion sig,Short genes enrichment sig
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