Protenix addition dev - #558

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nan5895 wants to merge 1794 commits into

protenix-addition_dev

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Commits on Jan 30, 2026

Merge branch 'dev' into clean-af2-outputs
JoseEspinosa
authored
edf4179
Merge branch 'dev' into maintainers
JoseEspinosa
authored
a624625

Commits on Feb 4, 2026

change param to save_intermediates
tlitfin
committed
caf62a9

Commits on Feb 5, 2026

clean up colabfold outputs and harmonize with other modes
tlitfin
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443e30d
Merge pull request #454 from tlitfin/clean-af2-outputs
JoseEspinosa
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99d65e2
Merge branch 'dev' into clean-cf-outputs
JoseEspinosa
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02b979e
Get number of sm directly from bash using nvidia-smi
JoseEspinosa
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cdd00c1
Add scape for bash variable
JoseEspinosa
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e676814
Get gpu name
JoseEspinosa
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19f794f
Merge branch 'fix_416' of https://github.com/JoseEspinosa/nf-core-proteinfold into fix_417
JoseEspinosa
committed
f94eccb

Commits on Feb 6, 2026

update changelog
tlitfin
committed
f575ab4
Get number of sm directly from bash
JoseEspinosa
committed
48991d8

Commits on Feb 9, 2026

Commits on Feb 10, 2026

Use torch to get number of sm, also check if there are more than one MIG slice
JoseEspinosa
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e33ceaf
Unify log messages when monkey patching nvmlDeviceGetNumGpuCores
JoseEspinosa
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ebe2e2d
Make lint happy
JoseEspinosa
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3e97574

Commits on Feb 11, 2026

Clean ESMFold ouputputs and have container triton cache writeable
keiran-rowell-unsw
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d567301
Update changelog
keiran-rowell-unsw
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d3b67b6
Whitespace..
keiran-rowell-unsw
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a118637
remove --boltz from --use_msa_server
keiran-rowell-unsw
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d72dc63
pass and 'intermediates' path to keep Boltz's nice folder structure
keiran-rowell-unsw
committed
c3e421b
consistent version
keiran-rowell-unsw
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61df600
Update changelog
keiran-rowell-unsw
committed
4b1d0e6
flatted top_ranked_structures like other modules
keiran-rowell-unsw
committed
db2ee6b
Merge pull request #458 from tlitfin/clean-cf-outputs
JoseEspinosa
authored
14bbeb4
Merge branch 'dev' into fix_417
JoseEspinosa
authored
a9bcb34
Merge pull request #465 from nf-core/keiran-rowell-unsw-patch-1
JoseEspinosa
authored
ba0bef8
Merge branch 'dev' into maintainers
JoseEspinosa
authored
0fb445e
Merge pull request #448 from JoseEspinosa/maintainers
JoseEspinosa
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4c90ee7
Merge remote-tracking branch 'upstream/dev' into fix_417
JoseEspinosa
committed
9d46cbc
Harmonised af3 outputs and added flaggable raw output (--save_intermediates)
JoseEspinosa
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2e4a83c
Add missing comma
JoseEspinosa
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7b3b347
sync changelog
keiran-rowell-unsw
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413dd46
Merge pull request #466 from Australian-Structural-Biology-Computing/clean-boltz-outputs
keiran-rowell-unsw
authored
11e9a81
Update conf/modules_esmfold.config

keiran-rowell-unsw
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JoseEspinosa
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3c8e1bb
remove containerOptions, prefer to add paths in-container for v2
keiran-rowell-unsw
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e81fcaf
Merge pull request #460 from JoseEspinosa/fix_417
JoseEspinosa
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288efdd
sync changelog
keiran-rowell-unsw
committed
e962fdf
fix mis-number and typo in changelog
keiran-rowell-unsw
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72a54bd
Merge branch 'dev' into clean-esmfold-outputs
keiran-rowell-unsw
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4d7277b
Remove cif sufix from converted pdb
JoseEspinosa
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b30ac47
Copy to raw after extract_metrics.py is run
JoseEspinosa
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597ebf4
Merge remote-tracking branch 'upstream/dev' into outputs
JoseEspinosa
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9bf7548
Make cache lenient
JoseEspinosa
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100de7c
HTML reports -> /reports not /generate
keiran-rowell-unsw
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5793fe7
update changelog
keiran-rowell-unsw
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81d524d
whitespace..
keiran-rowell-unsw
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03579a2
Harmonised HF3 outputs and added flaggable raw output
jscgh
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9722fa0
Harmonised RFAA outputs and added flaggable raw output
jscgh
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55547c6
Updated changelog
jscgh
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bde31a8
Merge branch 'dev' of github.com:nf-core/proteinfold into reports-in-reports
keiran-rowell-unsw
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31600d0
fix changelog
keiran-rowell-unsw
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44e4e6f
fix changelog
keiran-rowell-unsw
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0e033e7

Commits on Feb 12, 2026

Merge pull request #469 from Australian-Structural-Biology-Computing/reports-in-reports
JoseEspinosa
authored
cb2ce2d
Merge branch 'dev' into clean-esmfold-outputs
keiran-rowell-unsw
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a1d1d4b
pass through --env paths only if singularity or apptainer
keiran-rowell-unsw
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6ad9d23
Merge branch 'clean-esmfold-outputs' of github.com:Australian-Structural-Biology-Computing/proteinfold into clean-esmfold-outputs
keiran-rowell-unsw
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67d80e1
Fix Boltz output PR #
keiran-rowell-unsw
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6760dc0
run pre-commit
keiran-rowell-unsw
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d753a06
trailing whitespace..
keiran-rowell-unsw
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4f938ab
Merge branch 'dev' into outputs
JoseEspinosa
authored
ad293fb
Update alphafold3 snapshots
JoseEspinosa
committed
6baa3c3
Add ptm and iptm to stub run of af3
JoseEspinosa
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5ccc215
Update alphafold3 not to break cache
JoseEspinosa
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7035a4c
Update snapshots after changing generate for report in output folder
JoseEspinosa
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1a6b4ad
Error if dbs with possible different names are not found
JoseEspinosa
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37400a8
Update more snapshots failing to new report output folder
JoseEspinosa
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45d7a22
Update changelog
JoseEspinosa
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588a90e
Apply suggestion from @vagkaratzas

JoseEspinosa
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vagkaratzas
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442f577
Merge pull request #468 from JoseEspinosa/outputs
JoseEspinosa
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ed8e7a4
Clean rosettafold2na outputs
JoseEspinosa
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4b3645d
Add helixfold3 nf-test and snapshots
JoseEspinosa
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02970d8
Add rosettafold-aa nf-test and snapshots
JoseEspinosa
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d74b76d
Add boltz nf-test and snapshots
JoseEspinosa
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372a510
Fix version reporting
JoseEspinosa
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f5e9eb8
Merge remote-tracking branch 'origin/rf2na_outputs' into nf-test
JoseEspinosa
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156a0a4
Remove empty lines
JoseEspinosa
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fcd5fae
Merge pull request #464 from Australian-Structural-Biology-Computing/clean-esmfold-outputs
JoseEspinosa
authored
d30acfa
Fix indent of heredoc
JoseEspinosa
committed
87e5166
Update changelog
JoseEspinosa
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34c7581
Make lint happy
JoseEspinosa
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7cbe054
Merge branch 'dev' into rf2na_outputs
JoseEspinosa
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733babb
Update esmfold snapshots
JoseEspinosa
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1a6a573
Remove todo leftover
JoseEspinosa
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6652594
Update esmfold snapshots again
JoseEspinosa
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5107559
Merge pull request #471 from JoseEspinosa/rf2na_outputs
JoseEspinosa
authored
20f04da
Merge remote-tracking branch 'upstream/dev' into nf-test
JoseEspinosa
committed
f6fb7f9
Add rosettafold2na nf-test and snapshots
JoseEspinosa
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2027019
Update changelog
JoseEspinosa
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2b5ec57
Update helixfold3 snapshots
JoseEspinosa
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f46b251
Update rosettafold_aa snapshots
JoseEspinosa
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b394095
Update rosettafold2na snapshots
JoseEspinosa
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36ff7b1
Update boltz test config and add snapshots
JoseEspinosa
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0c410ad
Make lint happy
JoseEspinosa
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b140e0f
Merge pull request #474 from JoseEspinosa/nf-test
JoseEspinosa
authored
ad39e09

Commits on Feb 13, 2026

Updated output.md
jscgh
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31a3214
Simplified output.md per https://github.com/nf-core/proteinfold/issues/470
jscgh
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a1cbfb0
Addressed comments with canonical format reference and example report plots
jscgh
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203103a
Screenshots of v2 plots in report
keiran-rowell-unsw
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918910f
Update images to v2 in output documentation
keiran-rowell-unsw
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bd166e9
Update output description for clarity
keiran-rowell-unsw
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9e5ce5b
Direct links to output spects
keiran-rowell-unsw
authored
d075829
Update output links and descriptions in documentation
keiran-rowell-unsw
authored
127ef6c
Updated changelog
jscgh
committed
aecae5c

Commits on Feb 16, 2026

Apply suggestions from code review

jscgh
and
JoseEspinosa
authored
35d733d
Moved mode-specific intermediates to relevant section in output.md
jscgh
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001e69f
Merge pull request #475 from Australian-Structural-Biology-Computing/update-output
JoseEspinosa
authored
6deb328
Add version reporting to boltz_fasta
JoseEspinosa
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3a04f0a
Fix version reporting for combine_uniprot
JoseEspinosa
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0393633
Fix version reporting for download_pdbmmcif
JoseEspinosa
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20d8b05
Fix version reporting for download_pdbmm_af3
JoseEspinosa
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480925b
Symlink rosettafold2na dockerfile to download_rna_databases
JoseEspinosa
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d8b27ac
Avoid alphafold3_params_path to be overwritten when set in test profile
JoseEspinosa
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6a09d94
Add version reporting to fasta2json
JoseEspinosa
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08c2d04
Add version reporting to fasta2yaml
JoseEspinosa
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73d028e
Add libraries version reporting to run_alphafold3
JoseEspinosa
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56a95cb
Add more libraries to version reporting for esmfold
JoseEspinosa
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29264f2
Echo unknown when no version detected for hmmsearch
JoseEspinosa
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2e5c704
Get rid of code generating versions.yml file
JoseEspinosa
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645ec27
Add scripts to parse fasta files for helixfold3 and rosettafold_all_atom
JoseEspinosa
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12c699c
Call scripts to convert fasta files
JoseEspinosa
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94cf939
Report commit hash as rosettafold_aa version
JoseEspinosa
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9fdf619
Report versions for helixfold3
JoseEspinosa
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691e3ae

Commits on Feb 17, 2026

Commits on Feb 18, 2026

Update snapshots
JoseEspinosa
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62bda3f
Set unknown for python version when running stubs, update snapshots
JoseEspinosa
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4542080
Update snapshot
JoseEspinosa
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ab98b8a
Apply review suggestions
JoseEspinosa
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7f32bf8
Merge pull request #481 from JoseEspinosa/fixes
JoseEspinosa
authored
96f9350
Update utils_nfschema to fix help message with strict syntax
JoseEspinosa
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9fa809b
Update changelog
JoseEspinosa
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ad13961
Update modules json
JoseEspinosa
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6716e25
Merge pull request #482 from JoseEspinosa/updates
JoseEspinosa
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c36513c
Move foldseek logic to post_processing subworkflow
JoseEspinosa
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bcb9e95
Declare skip_foldseek parameter in schema and nextflow.config
JoseEspinosa
committed
b836ed9

Commits on Feb 20, 2026

Set aria2 time to a sensible value
JoseEspinosa
committed
b5a9cfd
Update changelog
JoseEspinosa
committed
8bb88b7
Merge pull request #483 from JoseEspinosa/updates
JoseEspinosa
authored
c341a08
Get rid of comment
JoseEspinosa
committed
6d9375a
Remove todos
JoseEspinosa
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9977f8d
Update changelog
JoseEspinosa
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0c79035
Update changelog
JoseEspinosa
committed
8a789b0
Use CUDA_VERSION ARG consistently in all dockerfiles
JoseEspinosa
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1ce3004
Standardise dockerfile labels using OCI specification
JoseEspinosa
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a942568
Bump version 2.0.0 in all dockerfiles
JoseEspinosa
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b4e3fbd
Update changelog
JoseEspinosa
committed
f608f20
Fix tyop in changelog
JoseEspinosa
committed
9d8b866

Commits on Feb 23, 2026

Commits on Feb 24, 2026

Merge pull request #495 from JoseEspinosa/i494
JoseEspinosa
authored
35fb79b
Merge branch 'dev' into fixes
JoseEspinosa
authored
1469230
Merge branch 'dev' into updates
JoseEspinosa
authored
72aa9ab
Merge pull request #493 from JoseEspinosa/fixes
JoseEspinosa
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ce80ab4
Fix rosettafold_aa publishing of DBs when usin prepare subworkflow
JoseEspinosa
committed
7d20568
Fix alphafold2 publishing of DBs when using prepare subworkflow
JoseEspinosa
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0dbbb63
Fix boltz publishing of DBs when using prepare subworkflow
JoseEspinosa
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19bf420
Fix esmfold publishing of DBs when using prepare subworkflow
JoseEspinosa
committed
1dababd

Commits on Feb 25, 2026

Merge branch 'dev' into updates
JoseEspinosa
authored
9a2f383
Fix helixfold publishing of DBs when using prepare subworkflow
JoseEspinosa
committed
dcd18bd
Patch unzip module
JoseEspinosa
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4e8ad28
Fix alphafold3 publishing of DBs when using prepare subworkflow
JoseEspinosa
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efde855
Update snapshot
JoseEspinosa
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2ab31ae
Fix rosettafold2na publishing of DBs when using prepare subworkflow
JoseEspinosa
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029491f

Commits on Feb 26, 2026

Merge pull request #492 from JoseEspinosa/updates
keiran-rowell-unsw
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3372055
Undo unzip patch and refactor how helixfold params are published and passed downstream
JoseEspinosa
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96a5e4e
Use params.db for rosettafold2na
JoseEspinosa
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524d972
Get rid of unzip patch
JoseEspinosa
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c474be2
Make lint happy
JoseEspinosa
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c98f984
Remove commited file by mistake
JoseEspinosa
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442dc8a
Update changelog
JoseEspinosa
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2d28898
Get rid of ENTRYPOINT in alphafold2 docker file
JoseEspinosa
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15d0771
Update changelog
JoseEspinosa
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9b0b62f
Merge branch 'dev' into fixes
JoseEspinosa
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7d1088a
Update alphafold2 download snapshot
JoseEspinosa
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6fb5a5c
Revert file deleted by mistake
JoseEspinosa
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bbb384c
Get rid of ENTRYPOINT in alphafold2_pred docker file
JoseEspinosa
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912e613

Commits on Feb 27, 2026

Commits on Mar 1, 2026

Fix merge error
JoseEspinosa
committed
4f4c8e2

Commits on Mar 2, 2026

Merge pull request #498 from JoseEspinosa/fixes
JoseEspinosa
authored
327f7a3
Merge branch 'dev' into updates
JoseEspinosa
authored
0ce1601
Add checks for DBs files provided using parameters (alphafold2)
JoseEspinosa
committed
6f21608
Apply review suggestions
JoseEspinosa
committed
b42e42d
Merge pull request #501 from JoseEspinosa/updates
JoseEspinosa
authored
2bcec65
Add checks for DBs files provided using parameters (colabfold)
JoseEspinosa
committed
93ba0e5
Add checks for DBs files provided using parameters (helixfold3)
JoseEspinosa
committed
9e51ed9

Commits on Mar 3, 2026

Add checks for DBs files provided using parameters (esmfold)
JoseEspinosa
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8990e7f
Add checks for DBs files provided using parameters (proteinfold3)
JoseEspinosa
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55acc69
Fix tyop in esmfold
JoseEspinosa
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c469d10
Remove checkIfExists for af3 rna dbs
JoseEspinosa
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9d34b43
Add checks for DBs files provided using parameters (boltz)
JoseEspinosa
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f853398
Add checks for DBs files provided using parameters (rosettafold_all_atom)
JoseEspinosa
committed
0181227
Add checks for DBs files provided using parameters (rosettafold2na)
JoseEspinosa
committed
7d1e746
Update changelog
JoseEspinosa
committed
ff3e32b
Merge remote-tracking branch 'upstream/dev' into fix_dw_paths
JoseEspinosa
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9a4ddac
Remove checkIfExists from dummy_db channel declaration, not needed and makes test fail
JoseEspinosa
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4288be9
Create fake dummy dbs to enable the running of the stub runs for tests
JoseEspinosa
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ddd499e
Rename to avoid name collision
JoseEspinosa
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53485f2

Commits on Mar 4, 2026

Make maxit binary executable when downloaded from s3
JoseEspinosa
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45ce71d
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-proteinfold into updates
JoseEspinosa
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f232716
Add helixfold3 test full config
JoseEspinosa
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f553095
Add use_gpu to full esmfold test
JoseEspinosa
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59c5b82
Merge pull request #504 from JoseEspinosa/fix_dw_paths
JoseEspinosa
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362c4c4
Merge remote-tracking branch 'upstream/dev' into updates
JoseEspinosa
committed
05602f8
Add rosettafold_aa full tests
JoseEspinosa
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e489d3f
Update tested full tests
JoseEspinosa
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b9e83f7
Add rosettafold2na full test
JoseEspinosa
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256bed9
Update full tests configs with path to s3 mini_dbs and other minor tweaks
JoseEspinosa
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fa19588
Correctly place test_full profiles
JoseEspinosa
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6017f02
Include gpu profile for full tests
JoseEspinosa
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8002df7
Update changelog
JoseEspinosa
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f7499b4
Update path to esmfold database to mini_dbs
JoseEspinosa
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99c668e
Merge pull request #508 from JoseEspinosa/updates
JoseEspinosa
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5516f9a
Setup gpu environment for full tests
JoseEspinosa
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8d3df12
Update changelog
JoseEspinosa
committed
34c1df3
Fix changelog comment
JoseEspinosa
committed
412a976

Commits on Mar 5, 2026

Commits on Mar 12, 2026

Commits on Mar 13, 2026

fix protenix output metrics extraction and versions report
nan5895
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be93464
add Dockerfile
nan5895
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e29c666
add Dockerfile
nan5895
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d5e9e36
changes md to add Change_logs and contributor
nan5895
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ba835ee
add test config and dummy data
nan5895
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c3038d6