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Bulk MultiQC reporting as a pipeline-installed Python module - #45

Merged

jscgh merged 36 commits into

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multiqc_bulk_report

Oct 1, 2026

Commits on Sep 23, 2026

feat(multiqc): package and install proteinfold MultiQC module in-pipeline

keiran-rowell-unsw
authored and
jscgh
committed
1e2e3f1
Remove facility logo for codebase PR

keiran-rowell-unsw
authored and
jscgh
committed
500b124
PYTHONPATH with pip install target

keiran-rowell-unsw
authored and
jscgh
committed
4f47313
docker container doesn't like shell substitution without escape chars

keiran-rowell-unsw
authored and
jscgh
committed
890668a
Fix git rebase messages that had been pulled into the install string

keiran-rowell-unsw
authored and
jscgh
committed
4705b78
Fix git rebase messages that had been pulled into the environment.yml

keiran-rowell-unsw
authored and
jscgh
committed
d15840b
ASBC CI doesn't allow 'dev' in version number

keiran-rowell-unsw
authored and
jscgh
committed
e983709
migrate away from old labelling and having plddt_raw etc

keiran-rowell-unsw
authored and
jscgh
committed
e1b4d77
Don't change the _msa.tsv renaming mv commands since I think they're use in comparison report

keiran-rowell-unsw
authored and
jscgh
committed
78cf423
remove duplicate multiqc config block

keiran-rowell-unsw
authored and
jscgh
committed
780043a
mutliqc -> plddt purge for proper multiqc bulk

keiran-rowell-unsw
authored and
jscgh
committed
982a132
migrate away from _raw. Metrics are just themselves

keiran-rowell-unsw
authored and
jscgh
committed
bea8aef
more explicit pattern matching

keiran-rowell-unsw
authored and
jscgh
committed
39564cd
hasattr breaks with new pydandtic model

keiran-rowell-unsw
authored and
jscgh
committed
746c721
config slip up

keiran-rowell-unsw
authored and
jscgh
committed
3de641a
tsv gets picked up

keiran-rowell-unsw
authored and
jscgh
committed
0d083bd
clean up files

keiran-rowell-unsw
authored and
jscgh
committed
0a39c9b
Restore pLDDT emits and module tests after rebase
jscgh
committed
092b3b1
Clean up stale MultiQC and Foldseek wiring
jscgh
committed
5cb1311
Updated snapshots
jscgh
committed
2c5f878
Update nf-core multiqc module to v1.35
jscgh
committed
61b8567
Fix linting for gh actions using old nf-core tools
jscgh
committed
a67c33f
Fix multiqc plugin install: add pip/pandas to module env
jscgh
committed
31950f4

Commits on Sep 24, 2026

try a manifest generated by qwen local agent
keiran-rowell-unsw
committed
873cdb4

Commits on Sep 25, 2026

use --cl-config to pass through meta.model
keiran-rowell-unsw
committed
e4502f5
function to pass through all mulitqc metrics
keiran-rowell-unsw
committed
fe804be
Revert "use --cl-config to pass through meta.model"
keiran-rowell-unsw
committed
8367be9

Commits on Sep 28, 2026

AF2 arity fixed
keiran-rowell-unsw
committed
795286c
lint
keiran-rowell-unsw
committed
c40227d

Commits on Sep 29, 2026

load model images, don't need double escape
keiran-rowell-unsw
committed
f35c880
restore MSA coverage and PAE container
keiran-rowell-unsw
committed
42b4657
update snapshots
keiran-rowell-unsw
committed
f2e71ac

Commits on Sep 30, 2026

Rework MultiQC to use stock module and custom content files
jscgh
committed
5a1e936
Complete to-dos for the generated reports
jscgh
committed
3c70b51

Commits on Oct 1, 2026