OpenPipelines.bio v1.0.0-rc4

BREAKING CHANGES

• query/cellxgene_census: Refactored the interface, documentation and internal workings of this component (PR #621).
  • Renamed arguments to align with standard OpenPipelines notations and cellxgene census API:
    • --input_database became --input_uri
    • --cellxgene_release became --census_version
    • --cell_query became --obs_value_filter
    • --cells_filter_columns became --cell_filter_grouping
    • --min_cells_filter_columns became --cell_filter_minimum_count
    • --modality became --output_modality
    • Removed --dataset_id since it was no longer being used.
    • Added --add_dataset_meta to add metadata to the output MuData object.
  • Documentation of the component and its arguments was improved.

BUG FIXES

• mapping/cellranger_multi: Fix the regex for the fastq input files to allow dropping the lane from the input file names (e.g. _L001) (PR #778).

• workflows/rna/rna_singlesample: Fix argument passing top_n_vars and obs_name_mitochondrial_fraction to the qc subworkflow (PR #779).