nf-core/proteinfold: Montseny Brook Newt

[2.0.0] - 2026-03-27 Enhancements & fixes [#177] - Fix typo in some instances of model preset alphafold2_ptm. [PR #178] - Enable running multiple modes in parallel. [#179] - Produce an interactive html report for the predicted structures. [#180] - Implement Foldseek. [#188] - Fix colabfold image to run in gpus. [PR ##205] - Change input schema from sequence,fasta to id,fasta. [PR #210] - Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure. [#214] - Fix colabfold image to run in cpus after #188 fix. [PR ##220] - Add RoseTTAFold-All-Atom module. [PR ##223] - Add HelixFold3 module. [#235] - Update samplesheet to new version (switch from sequence column to id). [#239] - Update alphafold2 standard mode Dockerfile. [#240] - Separate download and input of pdb mmcif files and obsolete database. [#229] - Add Boltz pipeline PR #227. [PR #249] - Update pipeline template to nf-core/tools 3.2.0. [PR #271] - Update RFAA and HF3 dockerfiles for quicker building and reduction in image size. [PR #274] - Simplify run_helixfold3 module and move arguments to modules.config. [#276] - Update helixfold3 dockerfile to make it compatible with H100 gpus. [#259] - Fix esmfold docker image to make it compatible with hopper GPU architecture. [#281] - Fix how argument --nv is passed to apptainer and singularity in the config. [PR #283] - Fixes to meet language server requirements and update link of the helixfold3 image. [PR #287] - Fixes symlinking of every mmcif file causing excess I/O. [#293] - Add back alphafold2_model_preset input to the call to run_alphafold2_pred. [PR #294] - Temporary downgrade of schema for passing CI tests with Nextflow edge version. [#272] - Colouring scheme conforming to AlphaFold2 confidence bands in html report. [PR #297] - Update pipeline template to nf-core/tools 3.2.1. [#273] - Fixes comparison report to correctly label msa coverage plots with corresponding method label. [#290] - Update Alphafold2 split images to make them compatible Hopper gpus. [PR #302] - Fix HF3 dbs and max_template_date. [PR #305] - Stop RFAA and HF3 symlinking scripts into workdir. [PR #306] - extract_output.py -> extract_metrics.py so pLDDT, MSA, PAE emitted as raw data .tsv files [PR #307] - Update Boltz-1 boilerplate and formatting. [PR #314] - Fix extract metrics for broken modules. [PR #312] - pTM & ipTM metrics now extracted [PR #315] - Add global db flag. [#263] - Removed broken colabfold options (auto and alphafold2) [PR #316] - Add process_gpu label to modules which use GPU. [PR #319] - Update boltz workflow to accept YAML as input. [PR #322] - Updates and reorganises the reference database directory structure. [PR #329] - Updates Boltz module to include Boltz-2. [PR #332] - Fix rare superposition bug in reports. [PR #333] - Updates the RFAA dockerfile for better versioning and smaller image size. [PR #335] - Update pipeline template to nf-core/tools 3.3.1. [PR #346] - Update pipeline template to nf-core/tools 3.3.2. [PR #351] - add chain-wise (i)pTM values and summary file for AF3-generation codes. [PR #354] - Update documentation with mode specific usage, capabilities. [PR #355] - Remove unneccesary params from Boltz and Helixfold3 modes. [PR #356] - Update AF2 defaults to use split mode and monomer_ptm model. [PR #357] - Update ColabFold module and image. [PR #359] - Harmonize parameters across modes. [PR #360] - Rename some DBs paths in the run modules so they are equal to those when DBs are downloaded. [PR #362] - Update boltz Dockerfile and image pinning specific version (2.0.3). [#364] - Move Dockerfiles to its corresponding module. [PR #370] - Fix extract chain metrics. [#367] - Boltz post-processing crashes. [#368] - Helixfold3 iPTM output missing when dealing with monomers make the process to fail. [#369] - Download all Alphafold3 DBs. [PR #350] - PAE of model 0 in Boltz HTML report, AlphaFold2 to pass the build system [PR #377] - Fix sequence msa synch for af2 split. [#380] - Fixes alphafold2_model_preset bug on retry. [#382] - Readds --full_dbs as a global option. [#378] - Fix nested obsolete pdbs from pdb70. [#388] - Fix colabfold prefix handling for output metrics. [#387] - Fix alphafold2_standard obsolete.dat path error. [#389] - Locked version numbers for HelixFold3 image to prevent bug caused by newer mamba versions. [PR #397] - Fix AF2 mgnify handling and improve version reporting for AlphaFold2 containers. [PR #398] - Fix issues with PREPARE_DBS subworkflows. [PR #399] - Update alphafold2 and alphafold2_pred Dockerfiles. [PR #404] - Boltz cache files moved to workdir, fixed version checks and Boltz stubRun. [#401] - Get rid of symlinking in the prediction tools processes when using "PREPARE_DBS" subworkflows [#410] - Switch RosettaFold2NA to Boltz-style multi-chain FASTA inputs and drop the interactions sheet. [PR #407] - Several changes to meet nf-core standards. [PR #409] - Force single pdb workflow outputs to return as a list [PR #396] - Split ColabFold into separate optimised containers with version pinning and significant size reduction. [#412] - Substitute "/" with "_" from fasta headers used to name files when using "--split_fasta". [PR #424] - Bump docker image version for release to 2.0.0, make code more friendly with Nextflow language server and other format issues/fixes. [#423] - Generate json workflow using bioflow-insight. [#425] - Pass as a single input channel fasta and features to get rid of meta2 in RUN_ALPHAFOLD2_PRED. [#440] - Support single-letter RF2NA type tags (type=P/R/D/S) in ROSETTAFOLD2NA FASTA headers. [PR #442] - Bump version 2.6.1 of nf-schema, Nextflow minimum version to 25.10.2 and update utils_nfschema_plugin subworkflow. [PR #443] - Add documentation guide for contributing new prediction modes. [PR #446] - Fix warnings from Nextflow lint. [PR #451] - Remove af2 multimer padding from msa plots. [#417] - Add boltz_use_kernels parameter to enable/disable using optimized Triton-based CUDA kernels CUDA kernels for Boltz inference. [#417] - Handle incompatible CUDA kernel errors in Boltz by automatically retrying with --use_kernels false. [#285] - Adding contributors to manifest. [PR #460] - Use nvidia-smi to obtain number of SM. [PR #454] - Update publishdir patterns for alphafold2 modules. [PR #458] - Update publishdir patterns for colabfold module. [#313] - Harmonize colabfold metrics extraction with other modes. [#455] - Fix colabfold monomer inheriting id from fasta header. [#457] - Fix colabfold multimer always downloading model weights. [PR #461] - Update publishdir patterns for HelixFold3 module [PR #462] - Update publishdir patterns for RoseTTAFold-All-Atom modules [PR #464] - Update publishdir patterns for Boltz module [PR #466] - Update module conf and publishdir patterns for ESMFold, pass through container args [PR #469] - HTML reports now in /reports output directory [PR #468] - Update publishdir patterns for Alphafold3 module [PR #471] - Update publishdir patterns for Rosettafold2na module [#473] - Add nf-test for rosettafold-aa, rosettafold2na, helixfold3 and boltz modes. [PR #475] - Update and simplify outputs.md with the latest structure [#480] - Make version reporting consistent for all local modules. [PR #482] - Update utils_nfschema to fix help message with strict syntax. [PR #483] - Move foldseek logic to the post_processing subworkflow and set sensible time to aria2 processes. [PR #492] - Clean TODOs from code and create issues instead for 2.0.0 release preparation. [PR #493] - Standardise Dockerfiles labels and bump version 2.0.0 to prepare release. [#494] - Publish Colabfold DBs when downloaded to be directly consumable using colabfold_db parameter. [#496] - Publish all DBs when downloaded to be directly consumable using the corresponding mode parameter. [#494] - Publish Colabfold DBs when downloaded to be directly consumable using colabfold_db parameter. [#499] - Get rid of ENTRYPOINT in alphafold2 dockerfiles. [PR #501] - Move python code of BOLTZ_FASTA to a python script in bin. [#503] - Add checkIfExists validation to user-provided database paths across all prepare DB subworkflows. [#507] - Implement missing full tests and check that the others work before release 2.0.0. [PR #509] - Setup gpu environment for AWS full tests. [#519] - Fix AWS full test before release 2.0.0. [PR #525] - Reduce AlphaFold2 multimer full test to a single replicate. [PR #531] - Fix alphafold2_random_seed type. [PR #538] - Bump version 2.0.0 for release preparation. [PR #563] - Fix boltz csv sync. [PR #570] - Update parameters table in changelog.