Release 5.1.0#468

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Vivian0105 wants to merge 190 commits into

Commits on Nov 19, 2025

Add novel allele and genotype inference processes to workflow
ayeletperes
committed

Commits on Jan 24, 2026

Merge pull request #435 from ayeletperes/master
ggabernet
authored

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

Merge branch 'novel-allele-and-genotype' of https://github.com/nf-core/airrflow into novel-allele-and-genotype
ggabernet
committed
connect genotyping workflow
ggabernet
committed
Update novel allele and genotype workflow
ayeletperes
committed
update container
ggabernet
committed
Merge pull request #442 from ggabernet/novel-allele-and-genotype
ayeletperes
authored
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

Commits on Feb 10, 2026

Commits on Feb 24, 2026

Merge branch 'novel-allele-and-genotype' into test_new_enchantr
Vivian0105
committed

Commits on Feb 25, 2026

modify novel_alleles_and_genotyping.nf
Vivian0105
committed

Commits on Feb 27, 2026

update to new test container
ggabernet
committed

Commits on Feb 28, 2026

Commits on Mar 3, 2026

parallelize makedb
ggabernet
committed

Commits on Mar 4, 2026

Commits on Mar 5, 2026

Commits on Mar 6, 2026

Commits on Mar 9, 2026

Commits on Mar 11, 2026

Update test snapshots
Tatiana Gelaf Romer
committed
Typo in changelog
Tatiana Gelaf Romer
committed
Update CHANGELOG.md

tgelafr-pfzr
and
ggabernet
authored
Merge pull request #453 from tgelafr-pfzr/bug/452-publishdir-overwrite
tgelafr-pfzr
authored

Commits on Mar 12, 2026

Merge branch 'dev' into novel-allele-and-genotype
Vivian0105
authored

Commits on Mar 13, 2026

Commits on Mar 16, 2026

Commits on Mar 17, 2026

Commits on Mar 18, 2026

Merge pull request #451 from nf-core/novel-allele-and-genotype
ggabernet
authored

Commits on Apr 7, 2026

refactor database fetching to support multiple sources and update AssignGenes configuration.
ayeletperes
committed

Commits on Apr 20, 2026

Update immcantation/airrflow container
Vivian0105
committed

Commits on Apr 23, 2026

Commits on Apr 28, 2026

Commits on Apr 29, 2026

Merge branch 'dev' into airrc-ref
ayeletperes
authored

Commits on Apr 30, 2026

Template update for nf-core/tools version 4.0.2
nf-core-bot
committed

Commits on May 1, 2026

Added genotyping test of single sample and genotyping tutorials
Vivian0105
committed

Commits on May 4, 2026

Commits on May 5, 2026

Commits on May 6, 2026

Commits on May 8, 2026

Commits on May 14, 2026

test new amulety version
ggabernet
committed

Commits on May 15, 2026

Commits on May 21, 2026

Commits on May 22, 2026

Commits on May 28, 2026

Merge pull request #469 from ggabernet/dev
ggabernet
authored

Commits on May 29, 2026

Modify dev based on comments from nf-core reviewers
Vivian0105
committed

Commits on Jun 1, 2026

Commits on Jun 3, 2026