openpipeline 0.4.0

NEW FUNCTIONALITY

• convert/from_bdrhap_to_h5mu: Merge one or more BD rhapsody outputs into an h5mu file.

• split/split_modalities: Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files.

• integrate/concat: Combine data from multiple samples together.

MINOR CHANGES

• mapping/bd_rhapsody_wta: Update to BD Rhapsody 1.10.1.

• mapping/bd_rhapsody_wta: Add parameters for overriding the minimum RAM & cores. Add --dryrun parameter.

• Switch to Viash 0.5.14.

• convert/from_bdrhap_to_h5mu: Update to BD Rhapsody 1.10.1.

• resources_test/bdrhap_5kjrt: Add subsampled BD rhapsody datasets to test pipeline with.

• resources_test/bdrhap_ref_gencodev40_chr1: Add subsampled reference to test BD rhapsody pipeline with.

• integrate/merge: Merge several unimodal .h5mu files into one multimodal .h5mu file.

• Updated several python docker images to slim version.

• mapping/cellranger_count_split: update container from ubuntu focal to ubuntu jammy

• download/sync_test_resources: update AWS cli tools from 2.7.11 to 2.7.12 by updating docker image

• download/download_file: now uses bash container instead of python.

• mapping/bd_rhapsody_wta: Use squashed docker image in which log4j issues are resolved.

BUG FIXES

• workflows/utils/WorkflowHelper.nf: Renamed utils.nf to WorkflowHelper.nf.

• workflows/utils/WorkflowHelper.nf: Fix error message when required parameter is not specified.

• workflows/utils/WorkflowHelper.nf: Added helper functions:

  • readConfig: Read a Viash config from a yaml file.
  • viashChannel: Create a channel from the Viash config and the params object.
  • helpMessage: Print a help message and exit.

• mapping/bd_rhapsody_wta: Update picard to 2.27.3.

DEPRECATED

• convert/from_bdrhap_to_h5ad: Deprecated in favour for convert/from_bdrhap_to_h5mu.

• convert/from_10xh5_to_h5ad: Deprecated in favour for convert/from_10xh5_to_h5mu.