Release version 3.2.1

Bugfixes

• Fixed a bug where log_file_path was not respected
• Removed NotImplementedError in genome_annotation base class

Release version 3.2.0

New Features

• Added support for DNase without footprinting step

Other

• Completed strict type checking for the entire codebase, enforced via precommit hooks and CircleCI

Release version 3.1.0

New Features

• Added accessioning for TF and histone ChIP runs with pBAM conversion

Release version 3.0.6

Bugfixes

• Replaced reference to fri_blacklist with fri_exclusion_list in ATAC align enrich QC

Release version 3.0.5

Bugfixes

• Changed pseudo-replicated peaks output type to pseudoreplicated peaks

Release version 3.0.4

Bugfixes

• Fixed a bug affecting long read RNA that would cause a TypeError due to trying to index Metadata directly instead of using Metadata.content

Release version 3.0.2

Bugfixes

• Fixed bug in ChIP/ATAC replicate counting

Release version 3.0.1

Bugfixes

• Fixed GCP backend label to match Caper

Release version 3.0.0

Breaking Changes

• Refactored File and Backend, breaking the old API. Methods to read files are now associated with the instances of File, not with Backend instance. Blob and File were merged into one class.

New Features

• pipeline_version is now posted for Analysis for all runs
• Added preferred_default for single replicated ChIP & ATAC
• Changed portal replicate counting to only consider released and in progress biological and technical replicates
• Added ability to accession local workflows

Bugfixes

• Removed posting of insert size plot for single ended WGBS

Release version 2.8.0

New Features

• Added ability to consider only files posted by the current accessioning run when generating derived_from. Updated dnase to use this mechanism for footprints bigBed files in order to connect to the correct empty bed file.