Consolidate bulk/single-cell TCR analysis into BULKTCR_ANALYSIS; remove dead cellranger/pseudobulk code - #97

Merged

dltamayo merged 18 commits into

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bulktcr-analysis-consolidation

Aug 22, 2026

Commits on Aug 17, 2026

Rename ANNOTATE_FROM_CONCAT to ANNOTATE, ANNOTATE to ANNOTATE_INGEST

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claude
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f08bdc7
Fix stale ANNOTATE_FROM_CONCAT references in comments (Task 1 review finding)

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9fe42f6
Extract BULKTCR_ANALYSIS subworkflow; remove cellranger from bulk

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269f66f
Wire SINGLECELL_WORKFLOW to call BULKTCR_ANALYSIS
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9245db7
Remove dead cellranger-pseudobulk files and config
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5822b92
Revert dev-speed test fixture swap before final review

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394c57b

Commits on Aug 18, 2026

Remove dead notebooks, plot modules, and orphaned config params

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af33826
Fix nextflow lint warnings: deprecated Channel factories, implicit closures,

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2deee3d

Commits on Aug 19, 2026

Rename .cirro to .cirro_bulk_analysis

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acb2b01
Delete unused GLIPH2 CLI reference/demo data (tests/test_data/gliph2-test-data/)

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e032397
Add single-cell Cirro launch profiles; remove dead pseudobulk profile

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24bae32
Remove dead legacy GLIPH2-CLI parameters

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06f5542
Fix vdj_chain_mode: wire into VDJ_QC instead of hardcoding

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16e58e3
Wire GLIPH2_TURBOGLIPH's tuning params as declared process inputs

dltamayo
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claude
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7f40e55

Commits on Aug 21, 2026