Fix '10x_multi_config' template generation for new 10x nomenclature - #1122
Merged
Merged
Conversation
…mmune Profiling with new nomenclature.
…i_config' template.
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Fixes a bug with template file generation for running Cellranger
multi, which was introduced in PR #1112 when updated nomenclature for 10x Genomics applications was added.When using the updated nomenclature for CellPlex, Flex and immune profiling data, the template configuration files for
cellranger multiwere not being created by thesetup_analysis_dirscommand due to a mismatch in library types (with the new library types not being recognised by themake_multi_config_templatefunction intenx/utils).The fix makes the following changes:
10x_multi_configcan now include an explicitlibrary_typeparameter, which is passed to themake_multi_config_templatefunction within thesetup_analysis_dirscommand (if specified; otherwise the library type falls back to the actual library type for the project);10x_multi_configtemplate has been removed from all other 10x Genomics applications;setup_analysis_dirsfor the new nomenclature.