issue #73: added barrnap rules

workflow/rules/annotation.smk

@@ -232,3 +232,27 @@ rule annotation_plasflow:
         "PlasFlow.py --input {input} --output {output.tmp} --threshold {params.threshold} && "
         "cut -f3,4,6- {output.tmp} > {output.tsv} && "
         "date) &> {log}"
+
+##################################################
+# rRNA genes
+
+rule annotation_barrnap:
+    input:
+        os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
+    output:
+        fa=os.path.join(RESULTS_DIR, "annotation/barrnap/{rtype}/{tool}/{kingdom}.fa"),
+        gff=os.path.join(RESULTS_DIR, "annotation/barrnap/{rtype}/{tool}/{kingdom}.gff")
+    log:
+        "logs/barrnap.{rtype}.{tool}.{kingdom}.log"
+    wildcard_constraints:
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS),
+        kingdom="|".join(config["barrnap"]["kingdom"])
+    threads:
+        config["barrnap"]["threads"]
+    conda:
+        os.path.join(ENV_DIR, "barrnap.yaml")
+    message:
+        "Annotation: rRNA genes w/ barrnap"
+    shell:
+        "(date && barrnap --threads {threads} --kingdom {wildcards.kingdom} --outseq {output.fa} < {input} > {output.gff} && date) &> {log}"
\ No newline at end of file

workflow/steps/annotation.smk

@@ -35,6 +35,13 @@ rule ANNOTATION:
         expand(
             os.path.join(RESULTS_DIR, "annotation/rgi/{rtype_tool}/rgi.txt"),
             rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
-        ) if "rgi" in config["steps_annotation"] else []
+        ) if "rgi" in config["steps_annotation"] else [],
+        # barrnap
+        expand(
+            os.path.join(RESULTS_DIR, "annotation/barrnap/{rtype_tool}/{kingdom}.{ext}"),
+            rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS],
+            kingdom=config["barrnap"]["kingdom"],
+            ext=["fa", "gff"]
+        ) if "barrnap" in config["steps_annotation"] else [],
     output:
         touch("status/annotation.done")