Assemble modelcif | Synthetic tests - #48
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…which might be a superset
…d ModelArchive deposition
…CIF spec next push
…e true modelCIF entries
…CIF that has 20 residues to match metrics DUMMY
…ies, and snapshots pass
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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- populate_modelcif.py: --seed accepts a rank_N-keyed *_seed.tsv (assets/DUMMY_SEED.tsv) or a single int; single-seed methods (alphafold2/colabfold/boltz via --random_seed) get a shared seed SoftwareParameter; multi-seed methods (alphafold3-style seed x sample filenames) get per-model seeds shown in model names, since the modelcif dumper registers only one QA metric type per class. - bin/utils.py: infer_model_seed() for AF3 'seed-N' and ColabFold '_seed_NNN' filenames. - Fix: modelcif System._before_write() only harvests parameter groups from system.software_groups; the container_image SoftwareWithParameters appended to system.software in 22aaf0b was silently dropped from the output mmCIF. - assemble_modelcif/main.nf: seed notes; stale TODOs refreshed.
…lcif.py - protocol: optional template_search_step (driven by software-details YAML) inserted upstream of the coevolution MSA step, with its own Data and shared step software. - per-program verified model facts (uses_templates, has_recycling, ColabFold has_relaxation) emitted as boolean SoftwareParameters; --param KEY=VALUE adds/overrides entries (ints, floats, bools coerced). - dummy software details: alphafold2 now carries a template_search_step. - CHANGELOG entry for the ASSEMBLE_MODELCIF feature batch. Co-Authored-By: pi <noreply@pi.dev>
…am keys - environment.yml: pin modelCIF to 1.7 (pip syntax, ==) so the conda-resolved versions match the recorded snapshots; regenerate the three versions.yml snapshot hashes accordingly. - populate_modelcif.py: --param use_templates now aliases to the canonical uses_templates key instead of adding a duplicate field. Co-Authored-By: pi <noreply@pi.dev>
TemplateSearchStep previously inherited the modeling Software, claiming
AlphaFold2 searched the templates. It now resolves a dedicated Software
from template_search_software.name (YAML) or --template_software
(the topic: val("template_search"), val(tool) emission), with version
from --template_version / YAML, drawn from the known search tools
(hhsearch/hhblits/jackhmmer/mmseqs2/AFDB). Falls back to the modeling
software group when the tool is unknown, preserving old behaviour.
- DUMMY_SOFTWARE_DETAILS: alphafold2 -> hhsearch, alphafold3 -> mmseqs2
(per upstream data pipelines), use_main_software false.
- new nf-test asserting the attribution.
Co-Authored-By: pi <noreply@pi.dev>
…Biology-Computing/proteinfold into assemble_modelcif
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Part implements an ASSEMBLE_MODELCIF{} process as sketched out https://github.com/orgs/nf-core/projects/151
assemble_modelcif_X has ext.args config files to test creation of .bcif, or PAE embedded or linked
Test data: the following .cif files and dictionaries are used for testing, but not included in the PR to avoid binaries and line count inflation, they may be included in in test-datasets/proteinfold
mmcif_ddl.sdbmmcif_ma.sdbmmcif_pdbx_v50.sdbma-atiya1-gk-01.cifDatabases: databases will not be handled in .data.Datagroup.ReferenceDatabasein this PR. populate_modelcif.py is getting quite long already. Plus, it's a separate concept that can tie into the work done for reference dataset at NCI.
nf-core#575 might make this database handling easier, if considered valuable