Issues

• Pipeline not properly creating output folders

  sunbeam-labs/sunbeam#625 · Filter by author ArieDash opened on Jun 16, 2026

• Prevent writing uncompressed fastq during cutadapt

  sunbeam-labs/sunbeam#624 · Filter by author naomiwilson opened on May 28, 2026

• Config cleanup needed

  sunbeam-labs/sunbeam#617 · Filter by author kylebittinger opened on Apr 10, 2026

• Double check sequences in default adapters file

  sunbeam-labs/sunbeam#615 · Filter by author kylebittinger opened on Apr 10, 2026

• kraken table taxonomy rank not assigned correctly with kraken database k2_standard_20251015

  sunbeam-labs/sunbeam#614 · Filter by author WeimingWHu opened on Apr 9, 2026

• Refactor decontam.py

  sunbeam-labs/sunbeam#613 · Filter by author kylebittinger opened on Apr 9, 2026

• Consider using samtools

  sunbeam-labs/sunbeam#612 · Filter by author kylebittinger opened on Apr 9, 2026
  1

• Consider replacing fastqc

  sunbeam-labs/sunbeam#611 · Filter by author kylebittinger opened on Apr 9, 2026
  1

• Consider installing snakemake-executor-plugin-slurm when the slurm profile is used to initialize a sunbeam project

  enhancement
  sunbeam-labs/sunbeam#596 · Filter by author Ulthran opened on Nov 17, 2025

• Preprocess report overcounting low-complexity reads

  bug
  Bug

  sunbeam-labs/sunbeam#592 · Filter by author naomiwilson opened on Nov 6, 2025

• Import behavior with editable install

  bug
  sunbeam-labs/sunbeam#583 · Filter by author Ulthran opened on Oct 15, 2025
  

• documentation update

  sunbeam-labs/sunbeam#580 · Filter by author MasonMandolfo opened on Oct 6, 2025
  2

• sbx_release_action

  enhancementgithub_actions
  sunbeam-labs/sunbeam#520 · Filter by author Ulthran opened on Jun 3, 2025
  

• Custom entry/exit points for extensions

  enhancement
  sunbeam-labs/sunbeam#503 · Filter by author Ulthran opened on May 5, 2025
  

• Check that extensions are up to date

  enhancement
  sunbeam-labs/sunbeam#495 · Filter by author Ulthran opened on Jul 18, 2024
  

• Better automatic resource allocation

  enhancement
  sunbeam-labs/sunbeam#492 · Filter by author Ulthran opened on Jun 25, 2024
  

• Allow for empty input fastqs to run without error

  enhancement
  sunbeam-labs/sunbeam#488 · Filter by author Ulthran opened on Apr 19, 2024
  

• Add --version arg to sunbeam extend

  enhancement
  sunbeam-labs/sunbeam#486 · Filter by author Ulthran opened on Apr 9, 2024
  

• Remove aggregate_reads step in decontam

  enhancement
  sunbeam-labs/sunbeam#484 · Filter by author Ulthran opened on Apr 4, 2024
  

• Remove cutadapt

  enhancement
  sunbeam-labs/sunbeam#483 · Filter by author Ulthran opened on Apr 4, 2024
  

• Make updates to work with AWS Batch

  enhancement
  sunbeam-labs/sunbeam#467 · Filter by author Ulthran opened on Apr 1, 2024
  

• Clean out old extensions

  sunbeam-labs/sunbeam#466 · Filter by author Ulthran opened on Mar 29, 2024
  

• Replace komplexity with heyfastq

  enhancement
  sunbeam-labs/sunbeam#426 · Filter by author Ulthran opened on Nov 20, 2023
  

• Sunbeam extensions should use builtin dependency handling

  sunbeam-labs/sunbeam#260 · Filter by author louiejtaylor opened on Dec 12, 2019