Issues

• Add nf-test coverage for the basecalling Nextflow workflow

  securebio/basecall-workflow#26 · Filter by author katherine-stansifer opened on May 14, 2026

• Add pytest coverage for automation/run_automation.py

  securebio/basecall-workflow#25 · Filter by author katherine-stansifer opened on May 14, 2026

• Migrate process shell: blocks to script: (Nextflow 25.04 deprecation)

  securebio/basecall-workflow#24 · Filter by author katherine-stansifer opened on May 13, 2026

• Update Dorado version?

  securebio/basecall-workflow#17 · Filter by author mikemc opened on Jan 7, 2026
  4

• Add options to not trim fastqs

  securebio/basecall-workflow#16 · Filter by author katherine-stansifer opened on Aug 11, 2025

• Add option to extract kit from POD5 files

  securebio/basecall-workflow#15 · Filter by author katherine-stansifer opened on Aug 11, 2025

• Fix silent basecalling fails

  securebio/basecall-workflow#12 · Filter by author katherine-stansifer opened on Jun 17, 2025

• Add a basecalling mode for direct RNA seq data

  enhancement
  Feature

  securebio/basecall-workflow#11 · Filter by author simonleandergrimm opened on Apr 23, 2025
  

• Maybe add batching back in.

  securebio/basecall-workflow#9 · Filter by author simonleandergrimm opened on Apr 1, 2025
  

• If we do more duplex seq: make sure the right pod5s are in each batch.

  securebio/basecall-workflow#6 · Filter by author simonleandergrimm opened on Feb 24, 2025