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fix: six bugs that break FORMAT_KEGG_DB and KEGG annotation pipeline #485

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Merged
madeline-scyphers merged 4 commits into from
May 14, 2026
Merged

fix: six bugs that break FORMAT_KEGG_DB and KEGG annotation pipeline #485

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743bf8e
fix(format-kegg-db): three bugs in format_kegg_database.py
ruben1294 Feb 24, 2026
3afbce8
fix(format-kegg-db): two bugs in format_kegg_db.nf
ruben1294 Feb 24, 2026
f4b2394
fix(dram): pass boolean string to FORMAT_KEGG_DB skip_gene_ko_link
ruben1294 Feb 24, 2026
77b79ae
Small updates to PR
madeline-scyphers May 14, 2026
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5 changes: 2 additions & 3 deletions bin/format_kegg_database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion bin/rule_parser
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Submodule rule_parser updated 12 files
+19 −22 .github/workflows/python-test.yml
+2 −2 .gitignore
+31 −0 .pre-commit-config.yaml
+1 −0 README.md
+2 −1 requirements.txt
+3 −1 requirements_dev.txt
+4 −1 src/rules.lark
+112 −54 src/rules.py
+1 −1 tests/data/basic_anno.tsv
+2 −2 tests/data/basic_rules.tsv
+2 −2 tests/data/compound_rules.tsv
+8 −6 tests/test_parsing.py
5 changes: 3 additions & 2 deletions modules/local/database/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions modules/local/database/format_kegg_db.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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@madeline-scyphers madeline-scyphers May 14, 2026

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Thanks for catching the mmseqs missing here. It should go in the environment file, and then we use wave cli to generate this container uri. So I went ahead and did that and updated it.

container "community.wave.seqera.io/library/python_scikit-bio_scipy_mmseqs2:00f5f2307075f0e0"

tag { ch_kegg_pep }

Expand All @@ -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
Expand Down
2 changes: 1 addition & 1 deletion workflows/dram.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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){
Expand Down
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