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Author Commit Message Date Builds
250+ commits behind default.
John Chilton
Hide tools producing collections in workflow editor. Output collections will require significant overhaul to workflow editor logic.
John Chilton
Update workflow extraction backend for output collections.
John Chilton
A simpler way to configure output pairs (exploiting static structure). See example and comments in test/functional/tools/collection_creates_pair_from_type.xml.
John Chilton
More configurable format and metadata handling for output collections. Imporvements to testing code.
John Chilton
Allow tools to output collections with a dynamic number of datasets. Models: Track whether dataset collections have been populated yet. Dataset collections are still effectively immutable once populated - but dynamic output collections require them to be sort of likely `final` fields in Java (analogy courtesy of JJ) - allowing them to be declared before they are initialized or populated. This is tracked by the `populated_state` field. Tools: Output collections can now d…
John Chilton
Allow tools to output collections with static or determinable structure. By "static" I mean tools such as a FASTQ de-interlacer that would produce a "paired" collection with two datasets everytime. By "determinable" I mean tools that perform N->N operations within the same job - such as a tool that needs to normalize a bunch of datasets all at once and not in separate jobs. (For N->N collection operations that should or can be done in N separate jobs tool authors should just write tools that operate over a dataset and produce a dataset and let the end-user 'map over' that operation.) There are still large classes of operations where the structure of the output collection cannot be pre-determined - such as splitting files (e.g. bam files by read group) - that are not implemented in this commit. Model: The models have been updated to do a more thorough job of tracking collection outputs. Jobs just producing HistoryDatasetCollectionAssociations works fine for simple jobs produc…