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Make lint happy
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JoseEspinosa committed Jun 11, 2024
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Expand Up @@ -39,31 +39,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Parameters

| Old parameter | New parameter |
| --------------------- | -------------------------------------------- |
| `--uniclust30` | |
| `--bfd` | `--bfd_link` |
| `--small_bfd` | `--small_bfd_link` |
| `--alphafold2_params`| `--alphafold2_params_link` |
| `--mgnify` | `--mgnify_link` |
| `--pdb70` | `--pdb70_link` |
| `--pdb_mmcif` | `--pdb_mmcif_link` |
| `--pdb_obsolete` | `--pdb_obsolete_link` |
| `--uniref90` | `--uniref90_link` |
| `--pdb_seqres` | `--pdb_seqres_link` |
| `--uniprot_sprot` | `--uniprot_sprot_link` |
| `--uniprot_trembl` | `--uniprot_trembl_link` |
| `--uniclust30_path` | `--uniref30_alphafold2_path` |
| `--uniref30` | `--uniref30_colabfold_link` |
| `--uniref30_path` | `--uniref30_colabfold_path` |
| | `--uniref30_alphafold2_link` |
| | `--esmfold_db` |
| | `--esmfold_model_preset` |
| | `--esmfold_3B_v1` |
| | `--esm2_t36_3B_UR50D` |
| | `--esm2_t36_3B_UR50D_contact_regression` |
| | `--esmfold_params_path` |
| | `--skip_multiqc` |
| Old parameter | New parameter |
| --------------------- | ---------------------------------------- |
| `--uniclust30` | |
| `--bfd` | `--bfd_link` |
| `--small_bfd` | `--small_bfd_link` |
| `--alphafold2_params` | `--alphafold2_params_link` |
| `--mgnify` | `--mgnify_link` |
| `--pdb70` | `--pdb70_link` |
| `--pdb_mmcif` | `--pdb_mmcif_link` |
| `--pdb_obsolete` | `--pdb_obsolete_link` |
| `--uniref90` | `--uniref90_link` |
| `--pdb_seqres` | `--pdb_seqres_link` |
| `--uniprot_sprot` | `--uniprot_sprot_link` |
| `--uniprot_trembl` | `--uniprot_trembl_link` |
| `--uniclust30_path` | `--uniref30_alphafold2_path` |
| `--uniref30` | `--uniref30_colabfold_link` |
| `--uniref30_path` | `--uniref30_colabfold_path` |
| | `--uniref30_alphafold2_link` |
| | `--esmfold_db` |
| | `--esmfold_model_preset` |
| | `--esmfold_3B_v1` |
| | `--esm2_t36_3B_UR50D` |
| | `--esm2_t36_3B_UR50D_contact_regression` |
| | `--esmfold_params_path` |
| | `--skip_multiqc` |

> **NB:** Parameter has been **updated** if both old and new parameter information is present.
> **NB:** Parameter has been **added** if just the new parameter information is present.
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