Improve for rule 'prokka'

metaphor/workflow/rules/annotation.smk

@@ -78,7 +78,6 @@ rule prokka:
         outfile="output/annotation/prokka/{binning_group}/{bin}/{bin}.fna",
     params:
         outdir=lambda w, output: str(Path(output.outfile).parent),
-        kingdom_cmd=lambda w, input: f"grep '{w.bin}' {input.bin_evals}",
         args=config["prokka"]["args"],
     wildcard_constraints:
         binning_group="|".join(binning_group_names),
@@ -94,8 +93,9 @@ rule prokka:
     shell:
         """
         # Get kingdom from bin eval file
-        kingdom=$({params.kingdom_cmd} | cut -f 5)
-        kingdom=$(echo $kingdom | head -c 1 | tr '[a-z]' '[A-Z]'; echo $kingdom | tail -c +2)
+        bin_clean=$(echo {wildcards.bin} | sed 's/_sub$//g')  # Remove '_sub' from corrected bins
+        kingdom=$(grep $bin_clean {input.bin_evals})
+        kingdom=$(echo $kingdom | cut -f 5 | head -c 1 | tr '[a-z]' '[A-Z]'; echo $kingdom | tail -c +2)
 
         prokka --outdir {params.outdir}     \
                --kingdom $kingdom           \