0.7.0

openpipelines 0.7.0

MAJOR CHANGES

• Removed bin folder. As of viash 0.6.4, a _viash.yaml file can be included in the root of a repository to set common viash options for the project.
  These options were previously covered in the bin/init script, but this new feature of viash makes its use unnecessary. The viash and nextflow should now be installed in a directory that is included in your $PATH.

MINOR CHANGES

• filter/do_filter: raise an error instead of printing a warning when providing a column for var_filer or obs_filter that doesn't exist.

BUG FIXES

• workflows/full_pipeline: Fix setting .var output column for filter_with_hvg.

• Fix running mapping/cellranger_multi without passing all references.

• filter/filter_with_scrublet: now sets use_approx_neighbors to False to avoid using annoy because it fails on processors that are missing the AVX-512 instruction sets.

• workflows: Updated WorkflowHelper to newer version that allows applying defaults when calling a subworkflow from another workflow.

• Several components: pin matplotlib to <3.7 to fix scanpy compatibility (see scverse/scanpy#2411).

• workflows: fix a bug when running a subworkflow from a workflow would cause the parent config to be read instead of the subworklow config.

• correction/cellbender_remove_background: Fix description of input for cellbender_remove_background.

• filter/do_filter: resolved an issue where the .obs column instead of the .var column was being logged when filtering using the .var column.

• workflows/rna_singlesample and workflows/prot_singlesample: Correctly set var and obs columns while filtering with counts.

• filter/do_filter: removed the default input value for var_filter argument.

• workflows/full_pipeline and workflows/integration: fix PCA not using highly variable genes filter.