This is a quick bandaid fix for #107. A more robust fix would involve reimplementing a lot of the CLI, and that is not worth it now when we are going to do so anyway when we switch to nextflow.
Issues
mostly fixes #107
PR Checklist
(~Strikethrough~ any points that are not applicable.)
[x] This comment contains a description of changes with justifications, with any relevant issues linked.
~[ ] Update docs if there are any API changes.~
[x] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/
Changes
This is a quick bandaid fix for #107. A more robust fix would involve reimplementing a lot of the CLI, and that is not worth it now when we are going to do so anyway when we switch to nextflow.
Issues
PR Checklist
(~Strikethrough~ any points that are not applicable.)
CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/