annotation: fixed rgi rule (processed input)

workflow/rules/annotation.smk

@@ -9,7 +9,7 @@ rule annotation_prodigal:
     output:
         os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype}/{tool}/proteins.faa")
     log:
-        "logs/prodigal.{rtype}.{tool}.log"
+        "logs/annotation.prodigal.{rtype}.{tool}.log"
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
@@ -31,10 +31,10 @@ rule annotation_rgi:
         db=os.path.join(DB_DIR, "rgi/card.json"),
         setup="status/rgi_setup.done" # NOTE: to make sure that the same DB is used for all targets
     output:
-        faa=temp(os.path.join(RESULTS_DIR, "annotation/rgi/{rtype}/{tool}/input.faa"))
+        faa=temp(os.path.join(RESULTS_DIR, "annotation/rgi/{rtype}/{tool}/input.faa")),
         txt=os.path.join(RESULTS_DIR, "annotation/rgi/{rtype}/{tool}/rgi.txt")
     log:
-        "logs/rgi.{rtype}.{tool}.log",
+        "logs/annotation.rgi.{rtype}.{tool}.log",
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
@@ -52,8 +52,8 @@ rule annotation_rgi:
         "sed 's/\*$//' {input} > {output.faa} && "
         "rgi database --version --local && "
         # NOTE: https://github.com/arpcard/rgi/issues/93: KeyError: 'snp' --> re-run
-        "rgi main --input_sequence {input.faa} --output_file {params.obname} --input_type protein --local -a {params.alignment_tool} --clean -n {threads} || "
-        "rgi main --input_sequence {input.faa} --output_file {params.obname} --input_type protein --local -a {params.alignment_tool} --clean -n {threads} && "
+        "rgi main --input_sequence {output.faa} --output_file {params.obname} --input_type protein --local -a {params.alignment_tool} --clean -n {threads} || "
+        "rgi main --input_sequence {output.faa} --output_file {params.obname} --input_type protein --local -a {params.alignment_tool} --clean -n {threads} && "
         "date) &> {log}"
 
 ##################################################
@@ -66,7 +66,7 @@ rule annotation_casc:
     output:
         os.path.join(RESULTS_DIR, "annotation/casc/{rtype}/{tool}/ASSEMBLY.POLISHED.results.txt")
     log:
-        "logs/casc.{rtype}.{tool}.log"
+        "logs/annotation.casc.{rtype}.{tool}.log"
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
@@ -88,10 +88,10 @@ rule annotation_minced:
         asm=os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.POLISHED.fasta"),
         jar=os.path.join(MOD_DIR, "minced/minced.jar")
     output:
-        txt=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.POLISHED.results.txt"),
-        gff=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.POLISHED.results.gff")
+        txt=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/minced.txt"),
+        gff=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/minced.gff")
     log:
-        "logs/minced.{rtype}.{tool}.log"
+        "logs/annotation.minced.{rtype}.{tool}.log"
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
@@ -116,7 +116,7 @@ rule annotation_plasflow:
         tmp=temp(os.path.join(RESULTS_DIR, "annotation/plasflow/{rtype}/{tool}/plasflow.tsv.tmp")),
         tsv=os.path.join(RESULTS_DIR, "annotation/plasflow/{rtype}/{tool}/plasflow.tsv")
     log:
-        "logs/plasflow.{rtype}.{tool}.log"
+        "logs/annotation.plasflow.{rtype}.{tool}.log"
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS)
@@ -146,7 +146,7 @@ rule annotation_barrnap:
         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"
+        "logs/annotation.barrnap.{rtype}.{tool}.{kingdom}.log"
     wildcard_constraints:
         rtype="|".join(READ_TYPES),
         tool="|".join(ASSEMBLERS),
@@ -166,7 +166,7 @@ rule annotation_barrnap:
 rule annotation_hmm_kegg:
     input:
         faa=os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype}/{tool}/proteins.faa"),
-        hmm=config["hmm"]["dbs"]["kegg"]
+        hmm=os.path.join(DB_DIR, config["hmm"]["kegg"])
     output:
         os.path.join(RESULTS_DIR, "annotation/hmm/kegg/{rtype}/{tool}/hmm.tblout")
     log: