Add IMGT, OGRDB, and airrc-imgt germline reference sources - #3
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Contribute germline reference sources that download the germline and emit it in the format nf-core/airrflow consumes: a reference_base of per-chain FASTAs and, with --igblast, an igblast_base of BLAST databases plus the NCBI internal_data / optional_file trees mirrored from NCBI. Germline sources are a new kind of source. SourceBase and its rearrangement -> AIRR -> samplesheet path are built for repertoire data, so a ReferenceSource base (Sources/Germline.py) reuses the download half of SourceBase but produces its output through buildReference and the Reference module, kept apart from Sources so the two stay free of an import cycle. Cli.handleDownload branches on source.output; the OAS path is untouched. - Sources/Imgt.py: GENElect per-chain fetch (V/D/J 7.14, constant 14.1, mouse light constant 7.5, translated V 7.3), second-<pre> extraction, and the 200-on-error trap the weekly canary relies on. - Sources/Ogrdb.py: api_v2 species/set/release resolution and the segment split (V and C gapped, D and J ungapped, delta D vs C by length). - Sources/AirrcImgt.py: the airrc-imgt blend, composed from the OGRDB and IMGT sources (immunoglobulin from OGRDB; TR and the remaining constants from IMGT; no amino acid V). - Reference.py and `sourcerer reference build`: validate a germline folder (a nested reference_base or a flat folder of FASTAs) and build the IgBLAST databases; --check validates without makeblastdb. --igblast builds with makeblastdb (fail-fast when absent); no new runtime dependencies. - Weekly check-apis workflow probes the live IMGT and OGRDB APIs. - Packaged schema snapshots, unit tests with offline fixtures, and docs (README, NEWS, usage/module pages, IMGT/OGRDB citing).
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Contribute germline reference sources that download the germline and emit it in the format nf-core/airrflow consumes: a reference_base of per-chain FASTAs and, with --igblast, an igblast_base of BLAST databases plus the NCBI internal_data / optional_file trees mirrored from NCBI.
Germline sources are a new kind of source. SourceBase and its rearrangement -> AIRR -> samplesheet path are built for repertoire data, so a ReferenceSource base (Sources/Germline.py) reuses the download half of SourceBase but produces its output through buildReference and the Reference module, kept apart from Sources so the two stay free of an import cycle. Cli.handleDownload branches on source.output; the OAS path is untouched.
sourcerer reference build: validate a germline folder (a nested reference_base or a flat folder of FASTAs) and build the IgBLAST databases; --check validates without makeblastdb. --igblast builds with makeblastdb (fail-fast when absent); no new runtime dependencies.