[1.1.0] - 2024-06-25

Credits

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

• Adam Talbot
• Athanasios Baltzis
• Björn Langer
• FriederikeHanssen
• Igor Trujnara
• Leila Mansouri
• Luisa Santus
• Matthias Hörtenhuber
• Maxime Garcia
• Júlia Mir Pedrol
• Robert Syme
• Ziad Al-Bkhetan

Thank you to everyone else who 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.

• First release within nf-core
• Includes AlphaFold2 and ColabFold protein structure prediction methods

Thanks to @maxulysse and @adamrtalbot for reviewing this release.