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nf-core/proteinfold: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[1.1.0] - 2025-06-25

Credits

Special thanks to the following for their contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

  • [#80] - Add accelerator directive to GPU processes when params.use_gpu is true.
  • [#81] - Support multiline fasta for colabfold multimer predictions.
  • [#89] - Fix issue with excessive symlinking in the pdb_mmcif database.
  • [PR #91] - Update ColabFold version to 1.5.2 and AlphaFold version to 2.3.2
  • [PR #92] - Add ESMFold workflow to the pipeline.
  • Update metro map to include ESMFold workflow.
  • Update modules to remove quay from container url.
  • [nf-core/tools#2286] - Set default container registry outside profile scope.
  • [PR #97] - Fix issue with uniref30 missing path when using the full BFD database in AlphaFold.
  • [PR #100] - Update containers for AlphaFold2 and ColabFold local modules.
  • [PR #105] - Update COLABFOLD_BATCH docker container, metro map figure and nextflow schema description.
  • [PR #106] - Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
  • [#108] - Fix gunzip error when providing too many files when downloading PDBMMCIF database.
  • [PR #111] - Update pipeline template to nf-core/tools 2.9.
  • [PR #112] - Use nf-validation plugin for parameter and samplesheet validation.
  • [#113] - Include esmfold dbs for full data sets.
  • [PR #114] - Update paths to test dbs.
  • [PR #117] - Update pipeline template to nf-core/tools 2.10.
  • [PR #132] - Remove lib/ directory.
  • [#135] - Reduce Alphafold Docker images sizes.
  • [#115] - Throw message error when profile conda is used.
  • [#131] - Add esmfold small tests.
  • [#144] - Force value channels when providing dbs (downloaded) in main.nf to enable the processing of multiple samples.
  • [#147] - Update modules to last version.
  • [#145] - Implement test to check the processes/subworkflows triggered when downloading the databases.
  • [#130] - Add --skip_multiqc parameter.
  • [PR #154] - Update pipeline template to nf-core/tools 2.14.1.
  • [#148] - Update Colabfold DBs.
  • [PR #159] - Update mgnify paths to new available version.
  • [PR ##163] - Fix full test CI.
  • [#150]] - Add thanks to the AWS Open Data Sponsorship program in README.md.
  • [PR ##166] - Create 2 different parameters for Colabfold and ESMfold number of recycles.

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
--num_recycle --num_recycles_colabfold
--num_recycles_esmfold
--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. NB: Parameter has been removed if parameter information isn't present.

1.0.0 - White Silver Reebok

Initial release of nf-core/proteinfold, created with the nf-core template.

Enhancements & fixes