updated annotation rules (not tested)

workflow/rules/annotation.smk

@@ -9,11 +9,11 @@ rule annotation_prodigal:
     output:
         os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype}/{tool}/proteins.faa")
     log:
-        out="logs/annotation_prodigal_{rtype}.{tool}.out.log",
-        err="logs/annotation_prodigal_{rtype}.{tool}.err.log"
+        out="logs/prodigal.{rtype}.{tool}.out.log",
+        err="logs/prodigal.{rtype}.{tool}.err.log"
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads: 1
     conda:
         os.path.join(ENV_DIR, "prodigal.yaml")
@@ -34,11 +34,11 @@ rule annotation_diamond_daa:
         # NOTE: use uncompressed DAA format; other formats can be derived using `diamond view`
         os.path.join(RESULTS_DIR, "annotation/diamond/{rtype}/{tool}/proteins.daa")
     log:
-        out="logs/annotation_diamond_{rtype}.{tool}.out.log",
-        err="logs/annotation_diamond_{rtype}.{tool}.err.log"
+        out="logs/diamond_daa.{rtype}.{tool}.out.log",
+        err="logs/diamond_daa.{rtype}.{tool}.err.log"
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads:
         config["diamond"]["threads"]
     params:
@@ -58,11 +58,11 @@ rule annotation_diamond_tsv:
     output:
         os.path.join(RESULTS_DIR, "annotation/diamond/{rtype}/{tool}/proteins.tsv")
     log:
-        out="logs/annotation_diamond_tsv_{rtype}.{tool}.out.log",
-        err="logs/annotation_diamond_tsv_{rtype}.{tool}.err.log"
+        out="logs/diamond_tsv.{rtype}.{tool}.out.log",
+        err="logs/diamond_tsv.{rtype}.{tool}.err.log"
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     params:
         # NOTE: For the used conda version, need to specify the entire column layout (outfmt) explicitly
         outfmt="6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen",
@@ -85,8 +85,8 @@ rule annotation_rgi_input:
     output:
         temp(os.path.join(RESULTS_DIR, "annotation/rgi/{rtype}/{tool}/input.faa"))
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     message:
         "RGI: create input FAA: {input}"
     shell:
@@ -99,8 +99,8 @@ rule annotation_rgi_db:
         archive=temp(os.path.join(DB_DIR, "rgi/card-data.tar.bz2")),
         json=os.path.join(DB_DIR, "rgi/card.json")
     log:
-        out="logs/annotation_rgi_db.out.log",
-        err="logs/annotation_rgi_db.err.log"
+        out="logs/rgi_db.out.log",
+        err="logs/rgi_db.err.log"
     params:
         db_url=config["rgi"]["db_url"]
     message:
@@ -119,11 +119,11 @@ rule annotation_rgi:
     output:
         os.path.join(RESULTS_DIR, "annotation/rgi/{rtype}/{tool}/rgi.txt")
     log:
-        out="logs/annotation_rgi_{rtype}.{tool}.out.log",
-        err="logs/annotation_rgi_{rtype}.{tool}.err.log"
+        out="logs/rgi.{rtype}.{tool}.out.log",
+        err="logs/rgi.{rtype}.{tool}.err.log"
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads:
         config["rgi"]["threads"]
     params:
@@ -154,8 +154,11 @@ rule casc:
     output:
         os.path.join(RESULTS_DIR, "annotation/casc/{rtype}/{tool}/ASSEMBLY.results.txt")
     log:
-        out="logs/annotation_casc_{rtype}.{tool}.out.log",
-        err="logs/annotation_casc_{rtype}.{tool}.err.log"
+        out="logs/casc.{rtype}.{tool}.out.log",
+        err="logs/casc.{rtype}.{tool}.err.log"
+    wildcard_constraints:
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads:
         config["casc"]["threads"]
     conda:
@@ -174,8 +177,11 @@ rule minced:
         txt=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.results.txt"),
         gff=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.results.gff")
     log:
-        out="logs/annotation_minced_{rtype}.{tool}.out.log",
-        err="logs/annotation_minced_{rtype}.{tool}.err.log"
+        out="logs/minced.{rtype}.{tool}.out.log",
+        err="logs/minced.{rtype}.{tool}.err.log"
+    wildcard_constraints:
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     conda: "../envs/analysis.yaml"
     shell:
         "(date && "
@@ -184,7 +190,7 @@ rule minced:
         "date) 2> {log.err} > {log.out}"
 
 ##################################################
-# PlasFlow
+# Plasmids
 
 rule annotation_plasflow_input:
     input:
@@ -192,8 +198,8 @@ rule annotation_plasflow_input:
     output:
         temp(os.path.join(RESULTS_DIR, "annotation/plasflow/{rtype}/{tool}/input.fasta"))
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads: 1
     params:
         script=os.path.join(SRC_DIR, "filter_fasta_by_length.pl"),
@@ -210,11 +216,11 @@ rule annotation_plasflow:
         tmp=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:
-        out="logs/annotation_plasflow_{rtype}.{tool}.out.log",
-        err="logs/annotation_plasflow_{rtype}.{tool}.err.log"
+        out="logs/plasflow.{rtype}.{tool}.out.log",
+        err="logs/plasflow.{rtype}.{tool}.err.log"
     wildcard_constraints:
-        rtype="|".join(config["assemblers"].keys()),
-        tool="|".join(["|".join(a) for a in config["assemblers"].values()])
+        rtype="|".join(READ_TYPES),
+        tool="|".join(ASSEMBLERS)
     threads: 1
     params:
         threshold=config["plasflow"]["threshold"]