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Add HelixFold3#223

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JoseEspinosa merged 76 commits intonf-core:devnf-core/proteinfold:devfrom Australian-Structural-Biology-Computing:add-helixfold3Australian-Structural-Biology-Computing/proteinfold_old:add-helixfold3Copy head branch name to clipboardFeb 21, 2025

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Commits

Commits on Oct 11, 2024

• Draft new file: run_helixfold3.nf

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Commits on Oct 14, 2024

• Cleaned up folders

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Commits on Nov 5, 2024

• 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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Commits on Jan 29, 2025

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

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Commits on Feb 12, 2025

• Updated module pathing to match nf-core

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• Added per nf-core modules standard

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Commits on Feb 13, 2025

• Added per nf-core modules standard

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Commits on Feb 19, 2025

• Merge branch 'dev' into add-helixfold3

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• Make lint happy

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• Fix errors due to merging online (missing curly brackets, etc.)

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• More linting

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• Linting is never happy

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• Remove comma introduced during merging

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• Provide gawk image for helixfold3 tests

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Commits on Feb 20, 2025

• Fixing samplesheet version and tests

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• It is nice not to make tyops

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Commits on Feb 21, 2025

• Apply suggestions from code review

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• Fixed schema

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• https://github.com/nf-core/proteinfold/pull/223#discussion_r1963371178

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• Merge remote-tracking branch 'old/add-helixfold3' into old-helixfold3

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