Issues

• Multiple pairs of fastq files corresponding to the same sample (run TRUST4)

  bug
  nf-core/airrflow#514 · Filter by author Vivian0105 opened on Oct 9, 2026

• Bug with default parameter initialization

  bug
  nf-core/airrflow#507 · Filter by author alexnater opened on Oct 6, 2026
  1

• Add RemoveContaminants to number of sequences plot in airrflow report

  nf-core/airrflow#505 · Filter by author janaHoffmann1 opened on Sep 28, 2026
  

• External software version list

  enhancement
  nf-core/airrflow#501 · Filter by author eba28 opened on Sep 1, 2026
  2

• Implement --save_intermediate_repertoires option

  enhancement
  nf-core/airrflow#491 · Filter by author ggabernet opened on Aug 3, 2026
  

• Adding consensus_count / umi_count filter

  enhancement
  nf-core/airrflow#484 · Filter by author lauratwomey opened on Jul 9, 2026
  8

• Consider replacing SAMPLESHEET_CHECK module with the checks in schema_input.json

  enhancement
  nf-core/airrflow#476 · Filter by author Vivian0105 opened on Jun 4, 2026 · Release 5.2.0
  1

• "cp -r enchantr" in enchantr modules is suboptimal on cloud executors

  enhancement
  nf-core/airrflow#475 · Filter by author Vivian0105 opened on Jun 3, 2026 · Release 5.2.0

• Replace some local modules with available nf-core modules

  enhancement
  nf-core/airrflow#474 · Filter by author Vivian0105 opened on Jun 3, 2026 · Release 5.2.0

• Save and read repertoire files in gzip format

  enhancement
  nf-core/airrflow#473 · Filter by author Vivian0105 opened on Jun 3, 2026 · Release 5.2.0

• Takara Bio MaxiSeq Human FFPE TCR+BCR (with UMIs) Protocol

  enhancement
  nf-core/airrflow#470 · Filter by author Vivian0105 opened on May 29, 2026

• Optimize several nf-core/airrflow steps to use less memory

  enhancement
  nf-core/airrflow#465 · Filter by author Vivian0105 opened on May 12, 2026

• Profile for Biomed2 protocol to run nf-core/airrflow pipeline from fastq files

  enhancement
  nf-core/airrflow#463 · Filter by author Vivian0105 opened on May 12, 2026
  

• Enhance metadata sheet validation

  enhancement
  nf-core/airrflow#457 · Filter by author ggabernet opened on Apr 23, 2026

• Airrflow parameter 'skip_report' does not work

  bug
  nf-core/airrflow#455 · Filter by author Vivian0105 opened on Mar 31, 2026
  

• Profile for QIAseq Targeted RNA Panel Human TCR protocol

  enhancement
  nf-core/airrflow#450 · Filter by author Vivian0105 opened on Mar 3, 2026
  

• update pRESTO modules to use gzipped files and port to nf-core

  enhancement
  nf-core/airrflow#444 · Filter by author ggabernet opened on Jan 30, 2026
  

• Add protocol profiles for ireceptor and adaptive

  enhancement
  nf-core/airrflow#433 · Filter by author ggabernet opened on Jan 14, 2026
  

• allow using AIRR-C reference data

  nf-core/airrflow#424 · Filter by author ggabernet opened on Oct 21, 2025
  

• Add simultaneous TCR and BCR processing

  enhancement
  nf-core/airrflow#419 · Filter by author TWV-GIT opened on Oct 13, 2025

• Add profile for data created using QIAseq Targeted RNA Panel Human TCR protocol

  enhancement
  nf-core/airrflow#415 · Filter by author Vivian0105 opened on Sep 5, 2025

• error when running airrflow with several fastqs per sample, and distinct(metadata) returns more than 1 row

  nf-core/airrflow#414 · Filter by author wvictor14 opened on Aug 29, 2025 · Release 4.4.0
  1

• Update Dowser lineage trees to accept multiple trait values

  enhancement
  nf-core/airrflow#411 · Filter by author ggabernet opened on Aug 7, 2025 · Release 5.1.0

• sans-umi workflow error with variable name

  bug
  nf-core/airrflow#410 · Filter by author ggabernet opened on Aug 7, 2025 · Release 4.4.0

• Add aligAIR into airrflow

  enhancement
  nf-core/airrflow#408 · Filter by author ggabernet opened on Jul 29, 2025