diff --git a/bin/format_kegg_database.py b/bin/format_kegg_database.py
index 5287c994..a7b76ef9 100755
--- a/bin/format_kegg_database.py
+++ b/bin/format_kegg_database.py
@@ -73,7 +73,7 @@ def process_kegg(
     else:
         kegg_mod_loc = kegg_loc
     # make mmseqsdb from modified kegg fasta
-    kegg_mmseqs_db = path.join(output_dir, "kegg.%s.mmsdb" % download_date)
+    kegg_mmseqs_db = path.join(output_dir, "kegg.mmsdb")
     create_mmseqs(
         kegg_mod_loc,
         kegg_mmseqs_db,
@@ -150,9 +150,8 @@ def main():
     )
     parser.add_argument(
         "--skip_gene_ko_link",
-        type=bool,
+        action="store_true",
         help="Skip gene KO link processing. If not passed in, `--gene_ko_link_loc` is required",
-        default=False,
     )
     parser.add_argument(
         "--output_dir", type=str, help="Path to the output directory", default="kegg"
diff --git a/bin/rule_parser b/bin/rule_parser
index 229917c6..ba7bab38 160000
--- a/bin/rule_parser
+++ b/bin/rule_parser
@@ -1 +1 @@
-Subproject commit 229917c6bcd1b24fc12bdb137e0e79d6db86a261
+Subproject commit ba7bab38b779cee69bf650adbdd8900243143fe4
diff --git a/modules/local/database/environment.yml b/modules/local/database/environment.yml
index 8262e5a5..9345601f 100644
--- a/modules/local/database/environment.yml
+++ b/modules/local/database/environment.yml
@@ -4,5 +4,6 @@ channels:
 
 dependencies:
   - python=3.10
-  - scikit-bio=0.5.7
-  - scipy=1.8.1
+  - scikit-bio=0.7.1
+  - scipy<2
+  - mmseqs2==18.8cc5c
diff --git a/modules/local/database/format_kegg_db.nf b/modules/local/database/format_kegg_db.nf
index 0e4c0971..7df1f74c 100644
--- a/modules/local/database/format_kegg_db.nf
+++ b/modules/local/database/format_kegg_db.nf
@@ -4,7 +4,7 @@ process FORMAT_KEGG_DB {
     errorStrategy 'finish'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/python_scikit-bio_scipy:0f89a100e990daf2"
+    container "community.wave.seqera.io/library/python_scikit-bio_scipy_mmseqs2:00f5f2307075f0e0"
 
     tag { ch_kegg_pep }
 
@@ -19,7 +19,7 @@ process FORMAT_KEGG_DB {
 
     script:
     """
-    if [ ${skip_gene_ko_link} ]; then
+    if [ "${skip_gene_ko_link}" = "true" ]; then
         echo "No Gene KO Link file provided. Running KEGG DB formatting without"
         format_kegg_database.py --kegg_loc ${ch_kegg_pep} --download_date ${kegg_download_date} --threads ${params.threads} --output_dir kegg --skip_gene_ko_link
     else
diff --git a/workflows/dram.nf b/workflows/dram.nf
index 53481ba2..62c3784a 100644
--- a/workflows/dram.nf
+++ b/workflows/dram.nf
@@ -212,7 +212,7 @@ workflow DRAM {
 
         gene_ko_link_f = params.gene_ko_link_loc && file(params.gene_ko_link_loc).exists() ? file(params.gene_ko_link_loc) : default_sheet
         kegg_download_date = params.kegg_download_date ? params.kegg_download_date : "''"
-        skip_gene_ko_link = params.skip_gene_ko_link ? 1 : 0
+        skip_gene_ko_link = params.skip_gene_ko_link ? "true" : "false"
         FORMAT_KEGG_DB( kegg_pep_f, gene_ko_link_f, kegg_download_date, skip_gene_ko_link )
 
     } else if (params.merge_annotations){