fix: repair moldb-enumerate-mols workflow and correct enumeration count#17
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enumerate_mols.nf was wired to nf-processes/rdkit/enumerate.nf, which wraps the top-level enumerate.py (SDF-only output). The downstream load_enum process (moldb.load_enums) expects tab-delimited smiles/id/code .cxsmi records, which moldb/enumerate.py already knows how to produce via its --output *.cxsmi mode, but no Nextflow process wrapped it. Added nf-processes/moldb/enumerate.nf to fill that gap and repointed the include. Also fixes two multi-channel-output call sites in enumerate_mols.nf (load_enum(enumerate.out) and enumerate.out.subscribe) that needed explicit [0]/[1] indices, matching the convention used elsewhere in this repo's .nf files. With the pipeline actually running end-to-end for the first time, the moldb-count-rows "enumeration" test's hardcoded expected count (514) turned out to be stale. Verified across 3 independent fresh-database runs that the real, reproducible count is 529, and updated the test. Verified with jote against a real Postgres instance: all 12 tests in manifest-moldb.yaml now pass end-to-end (previously blocked at test 5/12). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This was referenced Jul 20, 2026
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Summary
moldb/enumerate_mols.nfwired itsenumerateprocess tonf-processes/rdkit/enumerate.nf, which wraps the top-levelenumerate.py— that script only ever writes real SDF blocks. The downstreamload_enumprocess (moldb.load_enums) expects tab-delimitedsmiles\tid\tcode.cxsmirecords instead, causingIndexError: list index out of rangeat runtime.moldb/enumerate.py(a separate, moldb-specific script) already supports exactly that.cxsmioutput mode, but no Nextflow process wrapped it. Addednf-processes/moldb/enumerate.nf(following the existingnf-processes/moldb/filter.nfpattern) and repointed theincludeinenumerate_mols.nf.enumerate_mols.nf(load_enum(enumerate.out)andenumerate.out.subscribe) that needed explicit[0]/[1]indices — same convention already used everywhere else in this repo's.nffiles (e.g.le_conformers.nf,frag-merge-pharmacophore.nf).moldb-count-rows'senumerationtest turned out to have a stale hardcoded expected count (514). Verified across 3 independent fresh-database runs that the real, reproducible count is 529 (not RDKit embedding randomness — identical every run), and updated the test accordingly.Test plan
jote --manifest data-manager/manifest-moldb.yamlagainst a real Postgres instance: all 12 tests now pass end-to-end (previously the run-group aborted at test 5/12, and even after the first fix, at test 6/12)🤖 Generated with Claude Code