Add cluster metrics viz - #11372

Merged

dbaku42 merged 70 commits into

nf-core:masterfrom

dbaku42:add-cluster-metrics-viz

May 24, 2026

Commits on May 6, 2026

New modules: cluster_metrics + cluster_viz
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9abde15
Move custom clustering modules under custom
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0320a41
Move custom clustering modules under custom
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e424338
Fix custom clustering module lint
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670bc33
Fix custom clustering module lint and snapshots
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3a26119
Address review comments for clustering custom modules
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e4877e4
Fix custom clustering module metadata
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7e19b22

Commits on May 7, 2026

Commits on May 8, 2026

Update modules/nf-core/custom/clustermetrics/main.nf

dbaku42
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pinin4fjords
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89287db
Update modules/nf-core/custom/clustermetrics/main.nf

dbaku42
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pinin4fjords
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d5ac668
Update modules/nf-core/custom/clustermetrics/main.nf

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pinin4fjords
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55e868a
Update modules/nf-core/custom/clustermetrics/main.nf

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pinin4fjords
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e492edb
Update modules/nf-core/custom/clustervisualiation/templates/cluster_viz.py

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pinin4fjords
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b8529f6
Update modules/nf-core/custom/clustervisualiation/templates/cluster_viz.py

dbaku42
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pinin4fjords
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12bb00d
Update modules/nf-core/custom/clustervisualiation/templates/cluster_viz.py

dbaku42
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pinin4fjords
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a4a01a3
fix: use template for cluster visualization module
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060eb5d
style: clean cluster visualization module main
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d48a224
fix: address reviewer feedback for cluster modules
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2d85309

Commits on May 11, 2026

Commits on May 12, 2026

fix: use docker:// prefix for singularity container to enable OCI conversion
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f240623
fix(custom/clustervisualization): set NUMBA_CACHE_DIR and MPLCONFIGDIR to fix numba caching in Singularity
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c46c26c
fix(custom/clustervisualization): move NUMBA_CACHE_DIR fix before any imports, and KMean n_init stable
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ad39971
Apply suggestion from @pinin4fjords

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pinin4fjords
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c8fec15
Apply suggestion from @pinin4fjords

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pinin4fjords
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3634466
Merge branch 'master' into add-cluster-metrics-viz
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0ca17c9
Prek and script fix
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6a7ac45

Commits on May 13, 2026

Fixed pandas series problem in cluster_metrics.py
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cddb5a8
fix: escape \n in f-strings for Groovy template compatibility
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4a72291
Format CUSTOM_CLUSTERMETRICS template with ruff
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2bf8afa
fix(clustermetrics,clustervisualization): update nf-test snapshots and test assertions
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fd15709
Merge branch 'master' into add-cluster-metrics-viz
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792373b
fix environment conflict
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6114ebd
feat: add custom clustering and metrics modules
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8348609
Merge branch 'master' into add-cluster-metrics-viz
dbaku42
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f1915bd

Commits on May 14, 2026

Clean up cluster modules and fix CI

pinin4fjords
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claude
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ac9a4ba
Use yaml.dump for versions.yml in cluster modules

pinin4fjords
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ea89bb2
Fix portability of CUSTOM_CLUSTERING and CUSTOM_CLUSTERVISUALIZATION CI

pinin4fjords
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51a747b
Tidy cluster module templates

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39baf33
Revert .gitignore drift unrelated to the PR

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465c8e4
Address findings from fresh review pass

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9870458
Align modules with nf-core spec: ext.args + dot-separated outputs

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3f5a5fa

Commits on May 19, 2026

chore: switch custom/clustering* modules to nf-core/test-datasets
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f858003
Merge branch 'master' into add-cluster-metrics-viz
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9ecf6d4
Merge branch 'master' into add-cluster-metrics-viz
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6aead49
update snapshot v2
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c840e84
Update test and snapshots
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05cbfc9
Merge branch 'master' into add-cluster-metrics-viz
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cda844d
restore test and snapshot
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a2617a1
fix(custom/clustervisualization): regenerate snapshot on Linux x86

pinin4fjords
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claude
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f5a2ba7
chore(custom/clustering): rename to custom/pcaclustering

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776f3d5

Commits on May 20, 2026

Add copyright and license headers
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4c50b31
Add copyright and license information
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fbcb1c3
Add copyright and license comments to cluster_viz.py
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874cc1b
Merge branch 'master' into add-cluster-metrics-viz
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8edc6c4
Rename pcaclustering in plink2pcaclustering
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32531f7
Merge branch 'master' into add-cluster-metrics-viz
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ba976f9
Fix tag for plink2pcaclustering in test file
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81f50f3
Merge branch 'master' into add-cluster-metrics-viz
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1ab3556
snapshot update plink2pcaclustering
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0625b62

Commits on May 21, 2026

refactor(custom/pcaclustering): accept generic sample_id features TSV

pinin4fjords
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5ae6c73
Merge pull request #1 from pinin4fjords/refactor/pcaclustering-generic-input
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e5429f1
Merge branch 'master' into add-cluster-metrics-viz
pinin4fjords
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e45e7d9
fix(custom/pcaclustering): point test at existing `test_features.tsv` fixture

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50d2883
refactor(custom/pcaclustering): drop hardcoded `sample_id` column name

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e7174e1
fix(custom/pcaclustering): preserve zero-padded numeric sample IDs

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f5edb63