feat: add save_cellranger_extra_files param#195
Merged
kelly-sovacool merged 5 commits intomainfrom Sep 15, 2025
Merged
Conversation
…ai, cloupe from cellranger_count
wong-nw
approved these changes
Sep 15, 2025
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changes
Add new parameter:
save_cellranger_extra_files.When false (default), only h5 files are published from cellranger_count.
When true, the bam, bai, & cloupe files are also published.
Issues
resolves #187
PR Checklist
(
Strikethroughany points that are not applicable.)[ ] Write tests usingnf-testfor any new features, bug fixes, or other code changes.[ ] If a new nextflow process is implemented, define the processcontainerandstub.CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/