removed problematic "--complete" argument for bakta (asssumes that ea…

…ch entry in the fasta is complete or circular)
metagenlab · Nov 26, 2024 · 718ba52 · 718ba52
1 parent 6a9d3f8
commit 718ba52
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/rules/annotation/bakta.rules b/rules/annotation/bakta.rules
@@ -36,7 +36,7 @@ rule annotate_with_bakta:
     shell:
         """
         export LC_ALL=C
-        bakta --force --threads {threads} --db {params[database]} --compliant --output samples/{wildcards.sample}/annotation --prefix {wildcards.sample} --strain {wildcards.sample} --genus '{params.genus}' --species '{params.spec}' --locus-tag 'CHUV' --complete {input[contigs]}
+        bakta --force --threads {threads} --db {params[database]} --compliant --output samples/{wildcards.sample}/annotation --prefix {wildcards.sample} --strain {wildcards.sample} --genus '{params.genus}' --species '{params.spec}' --locus-tag 'CHUV' {input[contigs]}
         unset LC_ALL
         """