nf-core/airrflow

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B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Stars: 82
Forks: 58
Open beginner issues: 0
Indexed issues: 44
Avg merge: 2d 23h
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Aug 28, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

44 open issues indexed

External software version list Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/airrflow#501 · 2 comments · Opened Sep 1, 2026
Implement `--save_intermediate_repertoires` option Open

enhancement

nf-core/airrflow#491 · 1 assignee · Opened Aug 3, 2026
Fix number of sequences plot in airrflow report Open

nf-core/airrflow#488 · 1 assignee · Opened Jul 29, 2026
Adding consensus_count / umi_count filter Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/airrflow#484 · 8 comments · Opened Jul 9, 2026
Consider replacing SAMPLESHEET_CHECK module with the checks in schema_input.json Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#476 · 1 comment · Opened Jun 4, 2026
"cp -r enchantr" in enchantr modules is suboptimal on cloud executors Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/airrflow#475 · Opened Jun 3, 2026
Replace some local modules with available nf-core modules Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#474 · Opened Jun 3, 2026
Save and read repertoire files in gzip format Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/airrflow#473 · Opened Jun 3, 2026
Takara Bio MaxiSeq Human FFPE TCR+BCR (with UMIs) Protocol Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#470 · Opened May 29, 2026
Optimize several nf-core/airrflow steps to use less memory Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/airrflow#465 · Opened May 12, 2026
Profile for Biomed2 protocol to run nf-core/airrflow pipeline from fastq files Open

enhancement

nf-core/airrflow#463 · 1 assignee · Opened May 12, 2026
Enhance metadata sheet validation Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

nf-core/airrflow#457 · Opened Apr 23, 2026
Airrflow parameter 'skip_report' does not work Open

bug

nf-core/airrflow#455 · 1 assignee · Opened Mar 31, 2026
Profile for QIAseq Targeted RNA Panel Human TCR protocol Open

enhancement

nf-core/airrflow#450 · 1 assignee · Opened Mar 3, 2026
Allow output AIRR with all subjects Open

enhancement

nf-core/airrflow#445 · 1 assignee · Opened Feb 2, 2026
update pRESTO modules to use gzipped files and port to nf-core Open

enhancement

nf-core/airrflow#444 · 1 assignee · Opened Jan 30, 2026
Add protocol profiles for ireceptor and adaptive Open

enhancement

nf-core/airrflow#433 · 1 assignee · Opened Jan 14, 2026
allow using AIRR-C reference data Open

nf-core/airrflow#424 · 2 assignees · Opened Oct 21, 2025
Add simultaneous TCR and BCR processing Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/airrflow#419 · Opened Oct 13, 2025
Add profile for data created using QIAseq Targeted RNA Panel Human TCR protocol Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/airrflow#415 · Opened Sep 5, 2025
error when running airrflow with several fastqs per sample, and distinct(metadata) returns more than 1 row Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/airrflow#414 · 1 comment · Opened Aug 29, 2025
Update Dowser lineage trees to accept multiple trait values Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#411 · Opened Aug 7, 2025
sans-umi workflow error with variable name Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

nf-core/airrflow#410 · Opened Aug 7, 2025
Add aligAIR into airrflow Open

enhancement

nf-core/airrflow#408 · 1 assignee · Opened Jul 29, 2025
Add pgen computation Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/airrflow#400 · Opened Jun 6, 2025
Process data from Parse Evercode paired TCR + WT Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/airrflow#397 · 1 comment · Opened Jun 6, 2025
Support other single-cell protocols Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/airrflow#394 · Opened May 30, 2025
Improve output documentation Open

enhancement

nf-core/airrflow#393 · 1 assignee · Opened May 30, 2025
Port modules to nf-core with nf-test Open

nf-core/airrflow#389 · 1 assignee · Opened Apr 29, 2025
Read per UMI report (split by locus or primer) Open

enhancement

nf-core/airrflow#372 · 1 comment · 1 reaction · 1 assignee · Opened Mar 25, 2025
move contaminant sequence detection to before collapsing duplicates Open

enhancement

nf-core/airrflow#355 · 1 assignee · Opened Oct 23, 2024
modify pRESTO collapseseq process to keep UMI annotations Open

enhancement

nf-core/airrflow#354 · 1 assignee · Opened Oct 23, 2024
Enhancements for TCR analysis (locus TR) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/airrflow#353 · Opened Oct 19, 2024
Add UMI barcode diversity reporting Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/airrflow#352 · Opened Oct 19, 2024
Filtering sequences belonging to the loci specified in the samplesheet only Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/airrflow#351 · Opened Oct 19, 2024
Add the calculations of physicochemical properties from alakazam Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/airrflow#326 · Opened Apr 22, 2024
Fetch other databases than IMGT: AIRR reference set Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#300 · Opened Jan 22, 2024
Add regions translations to final repertoire table Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/airrflow#298 · Opened Jan 18, 2024
Report findthreshold should report chosen threshold Open

enhancement

nf-core/airrflow#272 · 1 assignee · Opened Jul 3, 2023
Test data Open

enhancement

nf-core/airrflow#253 · 1 assignee · Opened Apr 21, 2023
Add remaining R scripts to EnchantR Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/airrflow#246 · Opened Mar 14, 2023
Add metada should add only metadata columns needed for the analyses Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/airrflow#230 · Opened Feb 13, 2023
Report primers in airrflow report Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/airrflow#193 · Opened Oct 25, 2022
Include other define clones algorithms Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/airrflow#28 · 1 comment · Opened Apr 8, 2019

nf-core/airrflow

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