Fix bulk Cirro pipeline config and OOM/resource issues - #102

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fix/bulk-cirro-config

Commits on Sep 17, 2026

Fix bulk Cirro form params rejected by nf-schema type validation

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1066226

Commits on Sep 23, 2026

Cirro configs: use run_<level> flags instead of deprecated workflow_level

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b6c9f00
Fix run_<level> flags being ignored when passed as false from Cirro

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7b52f8a
Fix RENDER_NOTEBOOK reading an unstaged samplesheet path on remote executors

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6bbe09f
Notebooks: default alias_col to sample name when samplesheet lacks it

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748dd36
Fix samplesheet_stats.csv losing its row labels

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6fdddc3
Give RENDER_NOTEBOOK more memory to fix OOM on patient-details report

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bb20f13
Trim inline comments added in this branch down to one line each

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d453be0

Commits on Sep 24, 2026

Commits on Sep 29, 2026

Fix template_discovery_brief's VDJdb section for airr-native input

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3c5aa46
Fix public-clones UpSet plot crash on single-patient datasets

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4ee93c2

Commits on Sep 30, 2026

Vectorize remaining .apply(axis=1) hotspots in overlap/discovery_brief notebooks

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a98a69c
RENDER_NOTEBOOK: scale resources per-notebook instead of a flat 16cpu/256GB

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a30f790
RENDER_NOTEBOOK: move resource tiering into conf/modules.config, shrink heavy tier

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89d4f61
Trim multi-line comments added this session down to one line each

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0115237
RENDER_NOTEBOOK: move template_details_sample into the 64GB tier

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a7e137b