Issues

• DESeq2: add support for interaction effects

  galaxyproject/tools-iuc#8907 · Filter by author pavanvidem opened on Nov 12, 2026

• auto_chr_bin_nbits in data_manager_star

  galaxyproject/tools-iuc#8898 · Filter by author lldelisle opened on Nov 10, 2026
  3

• Autoupdate errors

  galaxyproject/tools-iuc#8880 · Filter by author gxydevbot opened on Nov 6, 2026
  2

  

• StringTie: help text gives wrong defaults for -f, -c and -M

  galaxyproject/tools-iuc#8867 · Filter by author jmchilton opened on Nov 5, 2026

• MultiQC: Qualimap option offers RNASeq output but silently drops it

  galaxyproject/tools-iuc#8866 · Filter by author jmchilton opened on Nov 5, 2026

• Add native SBDI submission and reannotation exporters from nf-core/ampliseq

  galaxyproject/tools-iuc#8835 · Filter by author nekrut opened on Oct 30, 2026

• BusyBox sort killed mid-pipe can leave a job green with empty or truncated output

  galaxyproject/tools-iuc#8805 · Filter by author richard-burhans opened on Oct 28, 2026
  1

• Tool request: PharmCAT's VCF Preprocessor utility

  tool request
  galaxyproject/tools-iuc#8794 · Filter by author jennaj opened on Oct 26, 2026

• snippy fails when reference file is of type ‘fasta.gz'

  galaxyproject/tools-iuc#8790 · Filter by author cat-bro opened on Oct 26, 2026

• "NCBI Datasets Genomes" tool redirects to ncbi.nlm.nih.gov instead of opening the tool form

  galaxyproject/tools-iuc#8789 · Filter by author vebaev opened on Oct 25, 2026
  2

• anndata 0.13.3 wrappers write nullable-string-array, which deployed scanpy 1.11.5 and scimap 2.1.0 wrappers cannot handle (scanpy 1.12.4 not deployed)

  galaxyproject/tools-iuc#8566 · Filter by author mvdbeek opened on Oct 20, 2026
  2

• Add Virmap

  tool request
  galaxyproject/tools-iuc#8521 · Filter by author tcollins2011 opened on Oct 12, 2026

• PICRUSt2 tools failing with blank input parameters when multiple file inputs are required

  galaxyproject/tools-iuc#8449 · Filter by author sakhabtoosh97-collab opened on Sep 22, 2026
  1

• Add remag

  tool request
  galaxyproject/tools-iuc#8413 · Filter by author bernt-matthias opened on Sep 11, 2026

• hyphy_fel: job exits 1 with no diagnostic — stderr contains only ignored OpenMPI warnings

  galaxyproject/tools-iuc#8392 · Filter by author afgane opened on Sep 5, 2026
  1

• kmindex query: multi-index ("all indices") query fans out to thousands of per-shard datasets with no aggregated output

  galaxyproject/tools-iuc#8389 · Filter by author nekrut opened on Sep 3, 2026

• Data Manager table values should identify data, not installation time

  galaxyproject/tools-iuc#8360 · Filter by author mvdbeek opened on Aug 28, 2026
  3

• [Tool] ViReMa (Virus Recombination Mapper) — bioconda recipe stuck at 0.6/python2 while upstream is at 0.33

  tool request
  galaxyproject/tools-iuc#8326 · Filter by author QuandongPan opened on Aug 19, 2026
  1

• Additional output for Stacks2: population

  galaxyproject/tools-iuc#8323 · Filter by author igormakunin2 opened on Aug 18, 2026
  1

• sra_tools: /http/timeout/read = "1000" in wrapper configfile sets a 1-second HTTP read timeout

  galaxyproject/tools-iuc#8316 · Filter by author pauldg opened on Aug 14, 2026

• Warning: TargetFinder stderr messages like "Use of uninitialized value $offset in substr at /usr/local/bin/targetfinder.pl line 537"

  galaxyproject/tools-iuc#8165 · Filter by author jennaj opened on Jul 6, 2026
  1

• Tool request: OpenFold3

  tool request
  galaxyproject/tools-iuc#8144 · Filter by author B0r1sD opened on Jun 26, 2026
  4

  

• CI setup for ITs

  galaxyproject/tools-iuc#8137 · Filter by author bernt-matthias opened on Jun 25, 2026
  3

• BayeScan tool : Define additional output files in the XML to enable workflow integration

  galaxyproject/tools-iuc#8131 · Filter by author GINAMO-EBVs opened on Jun 22, 2026
  4

• bug for FCS-GX

  galaxyproject/tools-iuc#8065 · Filter by author jaredbernard opened on Jun 4, 2026
  1