Release openpipeline 0.4.0 · openpipelines-bio/openpipeline

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.

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.

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.

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.