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Add HelixFold3#223

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jscgh wants to merge 156 commits intonf-core:devnf-core/proteinfold:devfrom Australian-Structural-Biology-Computing:add-helixfold3Australian-Structural-Biology-Computing/proteinfold_old:add-helixfold3Copy head branch name to clipboard

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Commits on Jul 29, 2024

• feat(katana.config): Created file katana.config

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• feat(katana.config): Added params for PBS queues

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• feat(katana.config): Added executor parameter to allow the use Katana scheduler

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• feat(katana.config): Added label configs for pushing to GPU partition

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• Merge pull request #1 from Australian-Structural-Biology-Computing/create-katana-config

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• feat(run_alphafold2): Added 'gpu_compute' label to the Alphafold process

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• Merge pull request #2 from Australian-Structural-Biology-Computing/add-labels-to-gpu-processes

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• feat(run_alphafold2_pred): Added 'gpu_compute' label

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• Merge pull request #3 from Australian-Structural-Biology-Computing/add-labels-to-gpu-processes

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• revert(run_alphafold2.nf): Removed GPU compute label from pipeline

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• Merge pull request #4 from Australian-Structural-Biology-Computing/add-labels-to-gpu-processes

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• Updated database links

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Commits on Jul 30, 2024

• Merge pull request #6 from Australian-Structural-Biology-Computing/database

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• feat(pf_files): Added testing files

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• Merge branch 'unsw-dev' into add-testing-files

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• Merge pull request #7 from Australian-Structural-Biology-Computing/add-testing-files

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• fix(proteinfold_test.sh): Made path to main.nf rel

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• revert(base.config): Changed executor back to local for testing as cluster tooling is incomlete

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• fix(proteinfold_test.sh): Changed mode to 'split_msa_production'

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Commits on Aug 1, 2024

• Merge pull request #2 from nf-core/master

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Commits on Aug 8, 2024

• fix(dbs.conf): Updated dbs.conf to work on UNSW infrastructure

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• fix(run_alphafold2_msa): Fixed incorrectly named files

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• fix(run_alphafold2_pred): Fixed incorrectly named files

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• fix(proteinfold_test.sh): Added singulairty argument

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• fix(samplesheet): Changed sample to a much smaller sample

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• fix(samplesheet): Changed sampel to a smaller sample

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• Merge pull request #8 from Australian-Structural-Biology-Computing/add-dbs-variables-to-msa-pipeline

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• feat(conf/dbs): Added variables for database names, and file names

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• feat(conf/dbs): Changed config paths to use database variables instead of hardcoded values

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• feat(run_alphafold2): Changed hardcoded paths to use variables and updated variable names

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• feat(run_alphafold2_msa): Removed hardcoded paths and changed variables

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• feat(run_alphafold2_msa): Added code from run_alphafold2.nf so that the script does not attempt to modify the existing database file

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• fix(conf/dbs): Changed variable names to have _prefix on the end to avoid conflicts with existing link variables

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• fix(conf/dbs): Changed existing variables to use new prefix variables

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• feat(nextflow.config): Added new param variables and defaults to the config file

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Commits on Aug 9, 2024

• feat(dbs): Made variables global

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Commits on Aug 16, 2024

• fix(dbs): Changed database directory default

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• feat(katana): Temporarily removed PBS job scheduling

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• fix(run_alphafold2): Fixed copy command to point to the correct directory

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• fix(run_alphafold2): Updated paths to point to the correct uniclust databse

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• fix(run_alphafold2): Fixed typo

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• feat(run_alphafold2): Added symlink for params file

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• feat(nextflow): Changed default to use GPU

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• feat(nextflow): Included katana config

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• feat(test): Added options to katana tests

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• revert(nextflow): Changed default GPU to false

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• revert(nextflow): Changed config back to base config

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Commits on Aug 23, 2024

• modified: conf/dbs.config

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Commits on Sep 5, 2024

• feat(katana): Added katana config

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Commits on Oct 10, 2024

• feat(style): pushing uncommited changes

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• Merge pull request #9 from Australian-Structural-Biology-Computing/clean-up-code

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Commits on Oct 11, 2024

• deleted: null/pipeline_info/ as per https://github.com/Australian-Structural-Biology-Computing/proteinfold/issues/11

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• Draft new file: run_helixfold3.nf

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Commits on Oct 14, 2024

• Merge branch 'unsw-dev' into add-rosettafold-all-atom

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• Initial draft rosettafold-all-atom.nf

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• Cleaned up folders

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Commits on Oct 16, 2024

• added workflows/rosettafold-all-atom.nf first draft

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• Updating main.nf to current master version and adding RFAA lines

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Commits on Oct 18, 2024

• Imported subworkflows and fixed formatting errors with RFAA lines

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Commits on Oct 21, 2024

• Adjusted naming to snake_case for compatibility, various minor changes to scripts to get RFAA working

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• Added schema support for rosetta_fold_all_atom mode and .yaml or .yml input files

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• modified: assets/schema_input.json

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• Updating input to work with .yaml https://github.com/Australian-Structural-Biology-Computing/proteinfold/issues/19 modified: assets/schema_input.json

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Commits on Oct 22, 2024

• Merge branch 'master' into add-rosettafold-all-atom

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• Merging

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• Updated naming scheme with merged changes

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• modified: modules/local/run_alphafold2.nf

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• For nf-core#197

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• Cleaned up files

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• Merge remote-tracking branch 'refs/remotes/origin/add-rosettafold-all-atom' into add-rosettafold-all-atom

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• Ran nf-core schema build

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• Merged with dev

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• Ran nf-core schema build

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• Dealing with permissions

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• Readding directory

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• modified: nextflow_schema.json

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• Removed deprecated "check_max"

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Commits on Oct 23, 2024

• Aligning input channels for RFAA

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• Aligning input channels for RFAA

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• Runs through rfaa -profile test and -stub successfully

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• modified: modules/local/run_rosettafold_all_atom.nf

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Commits on Oct 28, 2024

• Debugging RFAA

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• Debugging RFAA

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Commits on Oct 29, 2024

• RFAA now working to produce structures

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Commits on Oct 30, 2024

• Modified rfaa output to properly emit PDB file

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• Fixed renaming pdb

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Commits on Nov 1, 2024

• Pipeline now completes successfully

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• Cleaned up test configs

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• Built schema as per CONTRIBUTING.md

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• Fixed db conflicts

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Commits on Nov 4, 2024

• Troubleshooting benchmarks and having jobs queued and run by nextflow

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• Removed leftover blast-2.2.6 references

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• Updated nextflow_schema

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• Katana HPC gpu compute option

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• Fixing crashes caused by HPC not being able to reach the online custom configs

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• Ran nf-core linter

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• deleted: .github/workflows/linting_comment.yml

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• Linting files

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Commits on Nov 5, 2024

• Genericised pdb emission

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• Merge branch 'add-rosettafold-all-atom' into add-helixfold3

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• Properly calls the HF3 container but cannot run through process yet

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Commits on Nov 6, 2024

• Updated apptainer image paths

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• HF3 is now able to start a run

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• First working version of HF3 See https://github.com/Australian-Structural-Biology-Computing/proteinfold/issues/18 Related to nf-core#211

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Commits on Nov 11, 2024

• Merged with nf-core/dev

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• Merged with dev

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Commits on Nov 12, 2024

• Schema updates

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• Fixing config lines

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• new file: conf/modules_helixfold3.config

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• Modified katana.config to allow for direct execution of jobs on k095 from nextflow run

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• Fixing left over merge lines and linting

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• Linting modified: .github/workflows/linting_comment.yml

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• Updated awsfulltest.yml

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• Passes linting

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• modified: conf/katana.config

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• Fixing file emit for hf3

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• Emits files including cif properly now

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Commits on Nov 13, 2024

• HF3 and RFAA now working with Katana OnDemand

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• New branch for aligning the new modules (RFAA & HF3) with the nf-core repo

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Commits on Nov 14, 2024

• Updated for running with configs

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Commits on Nov 15, 2024

• Overhauled helixfold3 db paths to match nf-core methods

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Commits on Nov 18, 2024

• Katana config

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• Merged with origin/align-modules-to-nf-core for new HF3 path variables

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• Updated schema with nf-core pipelines schema build

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Commits on Nov 19, 2024

• Updated schema with nf-core pipelines schema build

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• nf-core pipelines lint passed

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Commits on Nov 21, 2024

• Merge remote-tracking branch 'upstream/dev' into add-helixfold3

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• Added Helixfold3 module

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• Aligned to nf-core dev

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• Started updating documentation

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• Added download functionality to prepare_helixfold3_dbs

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• Added variables for downloading hf3 dbs

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• DBs working

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• Fixed maxit-src

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• Updated files

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• Aligning files

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• schema_input.json added backwards compatibility to sequence columns

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Commits on Nov 22, 2024

• Test profiles added to nextflow.config

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Commits on Nov 28, 2024

• Aligned with dev

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• Merge remote-tracking branch 'upstream/dev' into add-helixfold3

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• Adding multiqc to hf3 module

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• Removed leftover RFAA files and variables

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Commits on Nov 29, 2024

• Working with multiqc enabled

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• Passes linting and tests

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• Aligned with nf-core dev

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• Merge remote-tracking branch 'upstream/dev' into add-helixfold3

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Commits on Dec 2, 2024

• Updated hf3 definition file

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• Updated hf3 definition file

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Commits on Dec 5, 2024

• Added HF3 Dockerfile

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• Prettier

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Commits on Dec 10, 2024

• Fixed hf3_environment.yaml missing packages

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• HF3 container path updated

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• HF3 dev path updated

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• Updated HF3 container to nf-core repo

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Commits on Dec 11, 2024

• Prettier

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Commits on Jan 16, 2025

• Merge remote-tracking branch 'upstream/dev' into add-helixfold3

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