Fix Nextflow pipeline wiring bugs blocking end-to-end runs - #7
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Implements docs/fix_plan.md items 1-7. Fixing items 1-3 (PRODUCE_NEO4J_FILES
and PROCESS_ALL_CONTACTS wiring) surfaced several more bugs in the same two
processes beyond the original review's scope, found by diffing each
process's declared Nextflow inputs/outputs/script args against what the
underlying Python scripts' argparse and to_csv() calls actually expect:
- PRODUCE_NEO4J_FILES: removed bogus --interpro_domain_ownership flag,
added missing --superfamily_domain_ownership/--gene3dsa_domain_ownership/
--scop2_sf_domain_ownership/--scop2_fa_domain_ownership flags, added
missing scop2_domains_info/scop2_domains_description inputs required by
produce_neo4j_files.py, and corrected its entire 58-entry output block
(wrong .csv.gz extension throughout, several renamed files, 13 files
missing entirely) to match the script's actual 71 output files -
cross-verified against import_neo4j_data.sh, which already referenced
the correct filenames.
- PROCESS_ALL_CONTACTS: fixed --contacts -> --contacts_file flag name,
added missing --scop2_descriptions_file flag and its input/channel
wiring, and fixed two output filename mismatches (gene3dsa_ not g3dsa_,
scop2_fa/scop2_sf not scop2b_fa/scop2b_sf).
- process_pdb_contacts.py: fixed missing comma silently merging "SCOP2"
"Pfam" into "SCOP2Pfam" in a domain filter, dropping real SCOP2/Pfam
annotations with no error.
- import_neo4j_data.sh: fixed copy-pasted IS_IN_SCOP_CLASS relationship
type used as the SCOP class node label instead of scopClass.
- nextflow.config: added missing params.scop2_descriptions_file.
- main.nf: replaced hardcoded author-specific Arpeggio conda env path
with the portable ${workflow.projectDir} pattern used elsewhere.
- docs/installation.md: updated stale Zenodo record/version reference to
match what the setup scripts actually download.
Item 8 (possible dead code: produce_minimal_neo4j_files.py,
produce_flat_files.py, import_neo4j_data_minimal.sh) intentionally left
untouched - needs an author decision, not a mechanical fix.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
main.nfand the Python scripts it calls, a Neo4j import mislabel, a silent-data-loss missing comma, a hardcoded conda path, and a stale Zenodo version reference.produce_minimal_neo4j_files.py,produce_flat_files.py,import_neo4j_data_minimal.sh) is intentionally left unresolved pending a decision on whether they're dead code or an undocumented minimal-install path.Test plan
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