Novel allele and genotype#443

Merged

ggabernet merged 31 commits into

nf-core:novel-allele-and-genotypefrom

ayeletperes:novel-allele-and-genotype

Feb 10, 2026

Commits on Jan 26, 2026

feat: Rename workflow to `NOVEL_ALLELES_AND_GENOTYPE` and integrate `CLONAL_ANALYSIS` subworkflow, feeding its repertoire output into genotype inference.
ayeletperes
committed

Commits on Jan 29, 2026

Update novel allele and genotype workflow
ayeletperes
committed
Merge remote-tracking branch 'ggabernet/novel-allele-and-genotype' into novel-allele-and-genotype
ayeletperes
committed
feat: Pass report logo to novel allele subworkflow and update segment handling arguments.
ayeletperes
committed
fix: specify explicit relative path for CLONAL_ANALYSIS module include
ayeletperes
committed
refactor: rename `NOVEL_ALLELES_AND_GENOTYPE` to `NOVEL_ALLELES_AND_GENOTYPING` subworkflow.
ayeletperes
committed
removed duplicated line
ayeletperes
committed
feat: Conditionally execute novel allele inference and reassignment steps, and update `enchantr`'s `outputby` parameter to `cloneby`.
ayeletperes
committed
feat: pass report logo image to NOVEL_ALLELES_AND_GENOTYPING process
ayeletperes
committed
Update schema and novel allele workflow parameters
ayeletperes
committed
update schema
ayeletperes
committed
update config for genotype
ayeletperes
committed
refactor: Replace `NOVEL_ALLELES_AND_GENOTYPING` with `NOVEL_ALLELES_AND_GENOTYPE` and update its conditional execution logic.
ayeletperes
committed
Fix: Correctly trigger novel allele and genotype inference when genotyping is enabled and add `skip_clonal_analysis` to test configuration.
ayeletperes
committed
refactor: Rename `NOVEL_ALLELES_AND_GENOTYPE` process to `NOVEL_ALLELES_AND_GENOTYPING`.
ayeletperes
committed
feat: Pass validated samplesheet as input to the NOVEL_ALLELES_AND_GENOTYPING process.
ayeletperes
committed
Remove the `reference` output from `reassign_alleles` and correct the `repertoire` output channel name to `repertoires` in `novel_alleles_and_genotyping`.
ayeletperes
committed
refactor: Simplify novel allele and genotyping subworkflow by removing samplesheet collection and update test configurations.
ayeletperes
committed
Remove the `force=FALSE` parameter from enchantr module calls.
ayeletperes
committed

Commits on Jan 30, 2026

Commits on Feb 5, 2026

feat: Refactor novel allele and genotyping subworkflow to pass reference FASTA within the main data tuple and introduce an `outputby` parameter for allele reassignment.
ayeletperes
committed