version.yml -> topic: channels migration - #625

Draft

keiran-rowell-unsw wants to merge 28 commits into

nf-core:devfrom

Australian-Structural-Biology-Computing:versions-yml-to-topic-channels

Commits on Jul 17, 2026

Justify model.AbInitioModel()
keiran-rowell-unsw
committed
45ac285
Add static RCSB CifCheck binary
keiran-rowell-unsw
committed
c1fc2a1
Complete validation suite including PDBx vs dummy and augumented valid ModelArchive deposition
keiran-rowell-unsw
committed
bf96b3e
assemble modelcif with minimal dummy metrics | Remove stub block since can't validate against 'toucht | asset metrics | use msa tool mapping
keiran-rowell-unsw
committed
11fcc24
re-parse .bcif to ensure it deserialised properly
keiran-rowell-unsw
committed
9e52ae4
Commence modelCIF .protocol() population | Add minimal entity and ModelArchive step classes into the DUMMY_MODELCIF that has 20 residues | Use DUMMY_SOFTWARE_DETAILS
keiran-rowell-unsw
committed
25ceac7
--all_structs flag in assemble_modelcif() tests against 5 ranked dummies, and snapshots pass
keiran-rowell-unsw
committed
48f4389
All modes -- versions.yml -> topic: migration | Accepted v2.1 incoming Boltz and Colabfold input and execution handling | AF3 code from CRG
keiran-rowell-unsw
committed
51f92f6
Acquiesce to modelcif_validate being a shell script so the version detection in topic: is same as others | Add the named _msa.tsv from contemporary approach to the RF2NA stub
keiran-rowell-unsw
committed
cdd6f63
remove real .cif files from /assets so the line count is less scary
keiran-rowell-unsw
committed
b2ff444
comment out MMCIF2PDB to appease linter and match removed from header
keiran-rowell-unsw
committed
293edfb
Add .branch guard to fit ch_input that linter was complain it sometimes could not be defined
keiran-rowell-unsw
committed
7668275
Drop (I think vestigial unused?) msa in calling fasta_to_boltz that really handles input not alignments
keiran-rowell-unsw
committed
d65d19b
provide empty MultiQC in POST_PROCESSING function signature before simplification refactor
keiran-rowell-unsw
committed
dab3bd9
Update cifcheck but the workflow lint fialiling should wait until dev -> master
keiran-rowell-unsw
committed
49c094d

Commits on Jul 20, 2026

Bump python version to one available on both biocontainers and quay.io
keiran-rowell-unsw
committed
2d482b2
Use .getText() to appease the CI system
keiran-rowell-unsw
committed
9c79c0b
remove merge comments from run_inference
keiran-rowell-unsw
committed
e313f53
fix tests
keiran-rowell-unsw
committed
5e86df5
lint expects strickly
keiran-rowell-unsw
committed
97d8132
fix whitespace
keiran-rowell-unsw
committed
b9d083c
lint expects strictly
keiran-rowell-unsw
committed
afe76e7
Make linter happy barring subworkflow movement
keiran-rowell-unsw
committed
20ae189
fix whitespace
keiran-rowell-unsw
committed
bad6570
Add versions.yml asserts to every test passing then: block to appease CI
keiran-rowell-unsw
committed
df26828
Add outdir to each when: test block's params
keiran-rowell-unsw
committed
e4a1a07
fix whitespace
keiran-rowell-unsw
committed
9aa6172
Sync local nf-core modules with up-to-date remote
keiran-rowell-unsw
committed
12091fa

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version.yml -> topic: channels migration - #625

version.yml -> topic: channels migration#625
keiran-rowell-unsw wants to merge 28 commits into
nf-core:devfrom
Australian-Structural-Biology-Computing:versions-yml-to-topic-channels

Commits on Jul 17, 2026

Justify model.AbInitioModel()

Add static RCSB CifCheck binary

Complete validation suite including PDBx vs dummy and augumented valid ModelArchive deposition

assemble modelcif with minimal dummy metrics | Remove stub block since can't validate against 'toucht | asset metrics | use msa tool mapping

re-parse .bcif to ensure it deserialised properly

Commence modelCIF .protocol() population | Add minimal entity and ModelArchive step classes into the DUMMY_MODELCIF that has 20 residues | Use DUMMY_SOFTWARE_DETAILS

--all_structs flag in assemble_modelcif() tests against 5 ranked dummies, and snapshots pass

All modes -- versions.yml -> topic: migration | Accepted v2.1 incoming Boltz and Colabfold input and execution handling | AF3 code from CRG

Acquiesce to modelcif_validate being a shell script so the version detection in topic: is same as others | Add the named _msa.tsv from contemporary approach to the RF2NA stub

remove real .cif files from /assets so the line count is less scary

comment out MMCIF2PDB to appease linter and match removed from header

Add .branch guard to fit ch_input that linter was complain it sometimes could not be defined

Drop (I think vestigial unused?) msa in calling fasta_to_boltz that really handles input not alignments

provide empty MultiQC in POST_PROCESSING function signature before simplification refactor

Update cifcheck but the workflow lint fialiling should wait until dev -> master

Commits on Jul 20, 2026

Bump python version to one available on both biocontainers and quay.io

Use .getText() to appease the CI system

remove merge comments from run_inference

fix tests

lint expects strickly

fix whitespace

lint expects strictly

Make linter happy barring subworkflow movement

fix whitespace

Add versions.yml asserts to every test passing then: block to appease CI

Add outdir to each when: test block's params

fix whitespace

Sync local nf-core modules with up-to-date remote