fix: update antismash resources

.tests/unit/gtdb_prep/data/config/lactobacillus_delbruecki/samples.csv

@@ -1,5 +1,5 @@
 genome_id,source,organism,genus,species,strain,closest_placement_reference,input_file
-GCF_000056065.1,ncbi,,,,,,
+GCA_000056065.1,ncbi,,,,,,
 GCF_000182835.1,ncbi,,,,,,
 GCA_000191165.1,ncbi,,,,,,
 GCF_000014405.1,ncbi,,,,,,

.tests/unit/gtdb_prep/expected/data/interim/gtdb/GCA_000056065.1.json

@@ -0,0 +1,22 @@
+{
+    "GCA_000056065.1":{
+        "assembly":"ASM5606v1",
+        "organism":"Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (firmicutes)",
+        "genus":"Lactobacillus",
+        "species":"delbrueckii",
+        "strain":"ATCC 11842",
+        "tax_id":"390333",
+        "refseq_category":null,
+        "refseq":"GCF_000056065.1",
+        "genbank":"GCA_000056065.1",
+        "assembly_type":"na",
+        "release_type":"major",
+        "assembly_level":"Complete Genome",
+        "genome_representation":"full",
+        "refseq_genbank_identity":"yes",
+        "biosample":"SAMEA3138258",
+        "submitter":"Genoscope",
+        "date":"2006-05-26",
+        "BioProject":"PRJNA16871"
+    }
+}

.tests/unit/test_gtdb_prep.py

@@ -20,15 +20,15 @@ def test_gtdb_prep():
         shutil.copytree(data_path, workdir)
 
         # dbg
-        print("data/interim/gtdb/GCF_000056065.1.json", file=sys.stderr)
+        print("data/interim/gtdb/GCA_000056065.1.json", file=sys.stderr)
 
         # Run the test job.
         sp.check_output(
             [
                 "python",
                 "-m",
                 "snakemake",
-                "data/interim/gtdb/GCF_000056065.1.json",
+                "data/interim/gtdb/GCA_000056065.1.json",
                 "-f",
                 "-j1",
                 "--target-files-omit-workdir-adjustment",

workflow/envs/antismash.yaml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - meme=5.5.2
+  - meme=4.11.2
   - python>=3.9
   - hmmer2
   - hmmer

workflow/rules/antismash.smk

@@ -61,13 +61,13 @@ elif antismash_major_version >= 7:
             as_js=directory(antismash_db_path / "as-js/0.13"),
             clusterblast=directory(antismash_db_path / "clusterblast"),
             clustercompare_mibig=directory(antismash_db_path / "clustercompare/mibig/3.1"),
-            comparippson_asdb=directory(antismash_db_path / "comparippson/asdb/3.0"),
+            comparippson_asdb=directory(antismash_db_path / "comparippson/asdb/4.0"),
             comparippson_mibig=directory(antismash_db_path / "comparippson/mibig/3.1"),
             knownclusterblast=directory(antismash_db_path / "knownclusterblast/3.1"),
             nrps_pks_stachelhaus=directory(antismash_db_path / "nrps_pks/stachelhaus/1.1"),
             nrps_pks_svm=directory(antismash_db_path / "nrps_pks/svm/2.0"),
             nrps_pks_transATor=directory(antismash_db_path / "nrps_pks/transATor/2023.02.23"),
-            pfam=directory(antismash_db_path / "pfam/34.0"),
+            pfam=directory(antismash_db_path / "pfam/35.0"),
             resfam=directory(antismash_db_path / "resfam"),
             tigrfam=directory(antismash_db_path / "tigrfam"),
         conda:

workflow/rules/common.smk

@@ -8,7 +8,7 @@ from pathlib import Path
 import peppy
 
 min_version("7.14.0")
-__version__ = "0.9.0"
+__version__ = "0.9.1"
 
 
 container: "docker://matinnu/bgcflow:latest"