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Add Trp-cage / 1L2Y test data for the colabfold module - #2354
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- pdb/1l2y.pdb: model 1 of the Trp-cage NMR structure (20 residues) - colabfold/trp_cage.a3m: single-sequence A3M query - colabfold/trp_cage_pdb_hits.m8: one BLAST-m8 template hit to 1l2y_A - colabfold/local_pdb.tar.gz: one-entry local PDB mirror (1l2y.cif) Used by the template tests of nf-core/modules colabfold/colabfold (#13066). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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… test every input - New colabfold/downloadmodels (COLABFOLD_DOWNLOADMODELS): downloads a parameter set once with colabfold's own download_alphafold_params(), which also writes the params/download*_finished.txt marker. Stub test. - colabfold/colabfold (COLABFOLD_COLABFOLD, moved from colabfold/): weights are a required input (--data); the empty-FASTA guard and its test are gone, the CPU test file is stub-only. - templates are staged as files into templates/, so the pdb70 index and PDB->mmCIF conversions colabfold writes there stay in the task dir. - The input also accepts a single A3M (colabfold names that query after the file); with a FASTA, --templates always queries the MSA server. - Stub names the files after the FASTA headers (or the A3M file name). - GPU tests take the weights from a setup block running COLABFOLD_DOWNLOADMODELS, and cover custom templates (1L2Y) and pdb_hits + local_pdb (via UNTAR) on Trp-cage; test data in nf-core/test-datasets#2354. - meta.yml: weights description (download marker), TSV for *.m8. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Test data for the template inputs of the
colabfold/colabfoldmodule (nf-core/modules#13066), requested in review: Trp-cage (PDB 1L2Y, 20 residues) so a GPU prediction takes seconds.data/proteomics/pdb/1l2y.pdbtemplatesinput (--custom-template-path); model 1 of 1L2Y, header records keptdata/proteomics/colabfold/trp_cage.a3m--templatesruns without the ColabFold MSA serverdata/proteomics/colabfold/trp_cage_pdb_hits.m8pdb_hitsinput (--pdb-hit-file), one hit to1l2y_Adata/proteomics/colabfold/local_pdb.tar.gzlocal_pdbinput (--local-pdb-path), one-entry mirrorlocal_pdb/1l2y.cifmade with ColabFold 1.5.5'sconvert_pdb_to_mmcifThe README of
data/proteomicsdescribes the files and how they were made. All three GPU tests of the module pass locally with these files (prediction finds1l2y_Aas template in both template tests).🤖 Generated with Claude Code