Merge upstream dev (2.0.0rc1) by jscgh · Pull Request #19 · Australian-Structural-Biology-Computing/proteinfold

jscgh · 2025-08-20T00:35:31Z

Full Changelog: 48e866a...nf-core:proteinfold:6923c119130b471b815d346747b2f2be6286763e

What's Changed

Bump version 1.2.0 dev by @JoseEspinosa in Bump version 1.2.0 dev nf-core/proteinfold#173
Fix uppercase model preset "alphaFold2-ptm" by @JoseEspinosa in Fix uppercase model preset "alphaFold2-ptm" nf-core/proteinfold#175
Enable running multiple modes in parallel by @ziadbkh in Enable running multiple modes in parallel nf-core/proteinfold#178
Produce an interactive html report for the predecited strucures by @ziadbkh in Produce an interactive html report for the predecited strucures nf-core/proteinfold#182
model names in lower case by @ziadbkh in model names in lower case nf-core/proteinfold#184
Adding foldseek to the workflow by @ziadbkh in Adding foldseek to the workflow nf-core/proteinfold#185
Merging template 3.0 by @JoseEspinosa in Merging template 3.0 nf-core/proteinfold#190
Merging template 3.0.2 by @JoseEspinosa in Merging template 3.0.2 nf-core/proteinfold#194
Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in Important! Template update for nf-core/tools v3.0.2 nf-core/proteinfold#193
Fix colabfold image to run in gpu environments with new cuda drivers by @JoseEspinosa in Fix colabfold image to run in gpu environments with new cuda drivers nf-core/proteinfold#195
Visualisation2 by @ziadbkh in Visualisation2 nf-core/proteinfold#196
Update schema by @luisas in Update schema nf-core/proteinfold#205
update nextflow version to 24.04.2 by @ziadbkh in update nextflow version to 24.04.2 nf-core/proteinfold#208
Moving post-processing logic to a subworkflow by @ziadbkh in Moving post-processing logic to a subworkflow nf-core/proteinfold#210
Refactoring of code to remove it from main and more by @JoseEspinosa in Refactoring of code to remove it from main and more nf-core/proteinfold#213
Fix colabfold image to run on cpus by @JoseEspinosa in Fix colabfold image to run on cpus nf-core/proteinfold#217
Multiple sequences as input and restructuring of output by @luisas in Multiple sequences as input and restructuring of output nf-core/proteinfold#204
adding nf-core logo to the reports by @ziadbkh in adding nf-core logo to the reports nf-core/proteinfold#225
Update samplesheet to version 1.2 by @JoseEspinosa in Update samplesheet to version 1.2 nf-core/proteinfold#236
Merge template version 3.1.1 by @JoseEspinosa in Merge template version 3.1.1 nf-core/proteinfold#238
Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in Important! Template update for nf-core/tools v3.1.1 nf-core/proteinfold#234
Separate mmcif_files from obsolete channels by @JoseEspinosa in Separate mmcif_files from obsolete channels nf-core/proteinfold#242
Add RoseTTAFold-All-Atom by @jscgh in Add RoseTTAFold-All-Atom nf-core/proteinfold#220
Add HelixFold3 by @jscgh in Add HelixFold3 nf-core/proteinfold#223
Updated AF2 standard Dockerfile by @jscgh in Updated AF2 standard Dockerfile nf-core/proteinfold#239
Merging-template-3.2.0 by @JoseEspinosa in Merging-template-3.2.0 nf-core/proteinfold#249
Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in Important! Template update for nf-core/tools v3.2.0 nf-core/proteinfold#243
Update dbs.config to correct pdb_mmcif_path by @Mitchob in Update dbs.config to correct pdb_mmcif_path nf-core/proteinfold#255
add mapping of identifier if legacy "sequence" identifier if "id" not… by @qclayssen in add mapping of identifier if legacy "sequence" identifier if "id" not… nf-core/proteinfold#267
Updated dockerfiles to shrink image sizes by @jscgh in Updated dockerfiles to shrink image sizes nf-core/proteinfold#271
Fix ESMFold Residue Numbering in COMPARE_STRUCTURES (issue Pipeline Fails at compare_structures During align_structures Step in Multimer Mode nf-core/proteinfold#257) by @Mitchob in Fix ESMFold Residue Numbering in COMPARE_STRUCTURES (issue #257) nf-core/proteinfold#270
Simplify helixfold3 by @jscgh in Simplify helixfold3 nf-core/proteinfold#274
Update helixfold3 image to make it compatible with H100 gpus by @JoseEspinosa in Update helixfold3 image to make it compatible with H100 gpus nf-core/proteinfold#278
Update esmfold image by @JoseEspinosa in Update esmfold image nf-core/proteinfold#280
Fix how nv argument is set in config by @JoseEspinosa in Fix how nv argument is set in config nf-core/proteinfold#282
Updates by @JoseEspinosa in Updates nf-core/proteinfold#283
Stops symlinking every mmcif_file by @jscgh in Stops symlinking every mmcif_file nf-core/proteinfold#287
Dowgrade schema version to 2.2.0 to pass CI test with Nextflow edge version by @JoseEspinosa in Dowgrade schema version to 2.2.0 to pass CI test with Nextflow edge version nf-core/proteinfold#294
fix wrong variable deletion from run_alphafold2_pred by @tlitfin-unsw in fix wrong variable deletion from run_alphafold2_pred nf-core/proteinfold#289
fix PDB parsing in generate_report.py by @tlitfin-unsw in fix PDB parsing in generate_report.py nf-core/proteinfold#264
Change html report color scheme to be consistent with standard by @tlitfin-unsw in Change html report color scheme to be consistent with standard nf-core/proteinfold#291
Add missing entries to changelog and fix linting by @JoseEspinosa in Add missing entries to changelog and fix linting nf-core/proteinfold#295
Merging-template-3.2.1 by @JoseEspinosa in Merging-template-3.2.1 nf-core/proteinfold#297
Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in Important! Template update for nf-core/tools v3.2.1 nf-core/proteinfold#296
Fix comparison report to correctly label msa coverage plots by @tlitfin-unsw in Fix comparison report to correctly label msa coverage plots nf-core/proteinfold#298
Update af2 split images by @JoseEspinosa in Update af2 split images nf-core/proteinfold#304
add error messages to schema for validation failures by @lee-t in add error messages to schema for validation failures nf-core/proteinfold#269
Fix HF3 dbs and max_template_date by @jscgh in Fix HF3 dbs and max_template_date nf-core/proteinfold#302
Stop RFAA and HF3 symlinking scripts into workdir by @jscgh in Stop RFAA and HF3 symlinking scripts into workdir nf-core/proteinfold#305
Adding boltz model - changes taken from pull#230 by @ziadbkh in Adding boltz model - changes taken from pull#230 nf-core/proteinfold#227
Common metric extraction [pLDDT, MSA, PAE]: extract_ouput.py -> extract_metrics.py in every program module by @keiran-rowell-unsw in Common metric extraction [pLDDT, MSA, PAE]: extract_ouput.py -> extract_metrics.py in every program module nf-core/proteinfold#306
Update Boltz-1 boilerplate and formatting by @jscgh in Update Boltz-1 boilerplate and formatting nf-core/proteinfold#307
Fix extract metrics for broken modules by @tlitfin-unsw in Fix extract metrics for broken modules nf-core/proteinfold#314
Adds process_gpu label by @jscgh in Adds process_gpu label nf-core/proteinfold#316
Add global db flag by @tlitfin-unsw in Add global db flag nf-core/proteinfold#315
Add alphafold3 by @JoseEspinosa in Add alphafold3 nf-core/proteinfold#252
remove unused input for mmseq by @ziadbkh in remove unused input for mmseq nf-core/proteinfold#318
Update boltz workflow to accept YAML as input by @Mitchob in Update boltz workflow to accept YAML as input nf-core/proteinfold#319
Refactor database paths by @jscgh in Refactor database paths nf-core/proteinfold#322
Updated RFAA dockerfile by @jscgh in Updated RFAA dockerfile nf-core/proteinfold#333
Merging template 3.3.1 by @JoseEspinosa in Merging template 3.3.1 nf-core/proteinfold#335
fix superpositon bug in reports by @tlitfin-unsw in fix superpositon bug in reports nf-core/proteinfold#332
zstd conda path fix by @vagkaratzas in zstd conda path fix nf-core/proteinfold#336
github snapshot diff fix by @vagkaratzas in github snapshot diff fix nf-core/proteinfold#345
Merging-template-v3.3.2 by @JoseEspinosa in Merging-template-v3.3.2 nf-core/proteinfold#346
Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in Important! Template update for nf-core/tools v3.3.2 nf-core/proteinfold#338
Update for Boltz-2 by @jscgh in Update for Boltz-2 nf-core/proteinfold#329
Add multimer confidence metrics (i)pTM to extraction by @keiran-rowell-unsw in Add multimer confidence metrics (i)pTM to extraction nf-core/proteinfold#312
Remove unneccesary params by @tlitfin-unsw in Remove unneccesary params nf-core/proteinfold#355
Update paths to some DBs to make them consistent with "PREPARE" subworkflows by @JoseEspinosa in Update paths to some DBs to make them consistent with "PREPARE" subworkflows nf-core/proteinfold#360
Chain-wise iPTM plaintext metrics by @keiran-rowell-unsw in Chain-wise iPTM plaintext metrics nf-core/proteinfold#351
Update boltz Dockerfile and image pinging specific version (2.0.3) by @JoseEspinosa in Update boltz Dockerfile and image pinging specific version (2.0.3) nf-core/proteinfold#362
Update AF2 defaults by @tlitfin-unsw in Update AF2 defaults nf-core/proteinfold#356
Update ColabFold by @jscgh in Update ColabFold nf-core/proteinfold#357
Update PREPARE_HELIXFOLD3 and ping specific version on Dockerfile by @JoseEspinosa in Update PREPARE_HELIXFOLD3 and ping specific version on Dockerfile nf-core/proteinfold#361
Move Dockerfiles to its corresponding module by @JoseEspinosa in Move Dockerfiles to its corresponding module nf-core/proteinfold#366
Harmonize parameters across modes by @tlitfin-unsw in Harmonize parameters across modes nf-core/proteinfold#359
Fix extract chain metrics by @tlitfin-unsw in Fix extract chain metrics nf-core/proteinfold#370

New Contributors

@jscgh made their first contribution in Add RoseTTAFold-All-Atom nf-core/proteinfold#220
@Mitchob made their first contribution in Update dbs.config to correct pdb_mmcif_path nf-core/proteinfold#255
@qclayssen made their first contribution in add mapping of identifier if legacy "sequence" identifier if "id" not… nf-core/proteinfold#267
@tlitfin-unsw made their first contribution in fix wrong variable deletion from run_alphafold2_pred nf-core/proteinfold#289
@lee-t made their first contribution in add error messages to schema for validation failures nf-core/proteinfold#269
@keiran-rowell-unsw made their first contribution in Common metric extraction [pLDDT, MSA, PAE]: extract_ouput.py -> extract_metrics.py in every program module nf-core/proteinfold#306
@vagkaratzas made their first contribution in zstd conda path fix nf-core/proteinfold#336

…-samples in Boltz for multiple models

…r-confidences Merge in add-metrics and Boltz updates

…sa reader

…r-confidences

…jscgh edits

… pdb (no maxit option)

…teinfold into updates

…update-colabfold Update ColabFold

…teinfold into updates

Update PREPARE_HELIXFOLD3 and ping specific version on Dockerfile

Move Dockerfiles to its corresponding module

Harmonize parameters across modes

Fix extract chain metrics

…uting#19 modified: assets/schema_input.json modified: modules/local/run_rosettafold_all_atom.nf modified: nextflow_schema.json

keiran-rowell-unsw and others added 30 commits May 19, 2025 14:07

AF2.3 extract pTM/iPTM

a63e873

Catch ColabFold monomer and multimer

0e2b372

add HF3 multimer processing, using [protein]-rank* directories

7ccd967

add Boltz ipTM/pTM metrics extraction. Haven't check with --diffusion…

fa22825

…-samples in Boltz for multiple models

Merge branch 'dev' of github.com:nf-core/proteinfold into add-multime…

04c0387

…r-confidences Merge in add-metrics and Boltz updates

id -> name for code clarity comes from --name arg

98806d4

Add (i)pTM extraction to AF non-split

854c81d

Add (i)pTM extraction to AF2 split

c3f299b

Add (i)pTM extraction to HF3

5280a4e

fix idx -> name mistake in read_npz

e7e1d51

Have Boltz use extract_metrics.py. Need to implement npz 'sequence' m…

09a9da4

…sa reader

note clarifying why two *.pkls went in wrong files

144e0d9

(i)pTM extraction in CHANGELOG

31e4956

Use actual PR number given

2524d3c

Fix prettier complaint about CHANGELOG

ae59a7e

Removed stray :w

9be7f1a

Add extract_metric to esmfold

e511555

extract_output corrected to extract_metrics in HF3

46bea81

Fixes HF3 not running extract_metrics within the right environment

f3d7028

Merge remote-tracking branch 'upstream/dev' into process_gpu

9d615fe

Merge branch 'dev' of github.com:nf-core/proteinfold into add-multime…

55d6eae

…r-confidences

id -> name after merge. Expand TODOs in prep for EXTRACT_METRICS process

e3e0bec

Merge - trailing whitespace

552af77

extract_metrics was merged into esmfold twice: from both tlitfin and …

1a30260

…jscgh edits

Fix boltz extract_metrics crashes

4f3d027

Fix HelixFold3 extract_metrics crash

d9e092a

Minor style change to run_alphafold2_pred to escape backslashes

24b40de

Add ipTM and pTM to HelixFold3 and fix numbering

8d416df

Fix boltz metric numbering

9b7fc25

Merge remote-tracking branch 'upstream/dev' into dev

d830605

JoseEspinosa and others added 27 commits August 6, 2025 13:56

Add helixfold3_maxit_src_link to nextflow schema

c42768a

Update snapshot

489b38f

Update snapshot

571af60

revert changes in helixfold3 as the newest version doesn't convert to…

889a75b

… pdb (no maxit option)

Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…

ed11e80

…teinfold into updates

Ping specific version of helixfold3

244eba9

Merge pull request #357 from Australian-Structural-Biology-Computing/…

59cbfdd

…update-colabfold Update ColabFold

Merge remote-tracking branch 'upstream/dev' into dockerfiles

cdcabf5

Merge remote-tracking branch 'upstream/dev' into updates

ccf21cf

Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…

38327bb

…teinfold into updates

Merge pull request #361 from JoseEspinosa/updates

d9c12e2

Update PREPARE_HELIXFOLD3 and ping specific version on Dockerfile

Merge remote-tracking branch 'upstream/dev' into dockerfiles

cb170ce

Merge pull request #366 from JoseEspinosa/dockerfiles

5be089c

Move Dockerfiles to its corresponding module

Merge remote-tracking branch 'upstream/dev' into harmonize-params

829c222

Add schema descriptions

7e0e296

Update snapshots

b449bf1

Harmonise naming of AF2 params

0e7cc1d

Added to changelog

448494f

Merge pull request #359 from tlitfin-unsw/harmonize-params

cb15d7a

Harmonize parameters across modes

Fix chainwise extract metrics

9f72b0a

Make iptm optional for monomer mode

99bf0e2

fix linting

e65a400

Merge branch 'dev' into fix-extract-chain

6dba1df

Update changelog

576e2a6

use csvwriter for extract_metrics

727db52

fix create_colabfold_index param

2c479b6

Merge pull request #370 from tlitfin-unsw/fix-extract-chain

6923c11

Fix extract chain metrics

jscgh self-assigned this Aug 20, 2025

jscgh merged commit 1a58b06 into Australian-Structural-Biology-Computing:master Aug 20, 2025
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Merge upstream dev (2.0.0rc1)#19

Merge upstream dev (2.0.0rc1)#19
jscgh merged 203 commits into
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