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Fix '10x_multi_config' template generation for new 10x nomenclature - #1122

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pjbriggs merged 5 commits into
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fix-10x_multi_config-template-generation
Dec 11, 2025
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pjbriggs merged 5 commits into
develfrom
fix-10x_multi_config-template-generation

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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 multi were not being created by the setup_analysis_dirs command due to a mismatch in library types (with the new library types not being recognised by the make_multi_config_template function in tenx/utils).

The fix makes the following changes:

  • The template specifications for 10x_multi_config can now include an explicit library_type parameter, which is passed to the make_multi_config_template function within the setup_analysis_dirs command (if specified; otherwise the library type falls back to the actual library type for the project);
  • The application definitions for CellPlex, Flex and immune profiling have been updated to explicit include this new parameter;
  • The 10x_multi_config template has been removed from all other 10x Genomics applications;
  • Unit tests have been added for the setup_analysis_dirs for the new nomenclature.

@pjbriggs
pjbriggs merged commit 8b5572b into devel Dec 11, 2025
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pjbriggs deleted the fix-10x_multi_config-template-generation branch December 11, 2025 14:23
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