All issues

Search results

Add nf-test coverage for the basecalling Nextflow workflow

Status: Open.

#26 In securebio/basecall-workflow;

· katherine-stansifer opened on May 14, 2026

Add pytest coverage for automation/run_automation.py

Status: Open.

#25 In securebio/basecall-workflow;

· katherine-stansifer opened on May 14, 2026

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

Status: Open.

#24 In securebio/basecall-workflow;

· katherine-stansifer opened on May 13, 2026

Update Dorado version?

Status: Open.

#17 In securebio/basecall-workflow;

· mikemc opened on Jan 7, 2026

Add options to not trim fastqs

Status: Open.

#16 In securebio/basecall-workflow;

· katherine-stansifer opened on Aug 11, 2025

Add option to extract kit from POD5 files

Status: Open.

#15 In securebio/basecall-workflow;

· katherine-stansifer opened on Aug 11, 2025

Fix silent basecalling fails

Status: Open.

#12 In securebio/basecall-workflow;

· katherine-stansifer opened on Jun 17, 2025

Add a basecalling mode for direct RNA seq data

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#11 In securebio/basecall-workflow;

· simonleandergrimm opened on Apr 23, 2025

Maybe add batching back in.

Status: Open.

#9 In securebio/basecall-workflow;

· simonleandergrimm opened on Apr 1, 2025

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

Status: Open.

#6 In securebio/basecall-workflow;

· simonleandergrimm opened on Feb 24, 2025