Automate external reference data download for the Nextflow pipeline - #8

Draft

m-crown wants to merge 8 commits into

fix/pipeline-wiring-bugsfrom

feature/reference-data-download

Commits on Aug 2, 2026

Automate external reference data download for the Nextflow pipeline

m-crown
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claude
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7cb5749
Confirm and fix SCOP2 download URLs in reference data manifest

m-crown
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claude
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aa6d034
Confirm and fix SCOP 1.75 and CCD download URLs in reference data manifest

m-crown
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claude
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d7e71a3
Confirm RHEA TSV URLs and add directory-target support for rd/ files

m-crown
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claude
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11048cb
Consolidate Pfam clan file handling onto Pfam's new single-file format

m-crown
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claude
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f3def53
Update plan doc status: RHEA rd/ and Pfam clan gaps resolved

m-crown
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claude
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7aa945e
Derive pubchem_substance_id_mapping.txt from NCBI's bulk CID-Identifiers file

m-crown
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claude
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5064db4
Update plan doc: pubchem gap resolved, zero manual entries remain

m-crown
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claude
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f6e91f3