Ben Sherman
Ben Sherman
The original output format created for this plugin could be improved in a number of ways, including: - list pipeline params - include task scripts The format is currently called...
The BCO project has a standard API endpoint for validation BCO manifests: https://biocomputeobject.org/api/docs/ According to the BCO maintainers there are two minor issues with the current BCO manifest: 1. URIs...
Add a test step to the github action that runs rnaseq-nf with every output format enabled. Will need to build and install the plugin. Also would be nice to remove...
PR #3 was originally going to add an RO crate manifest alongside the BCO manifest, but it turns out the RO crate example I was working off of was outdated....
The usual pattern to render a JSON file is to create the equivalent data structure in Groovy code, render it to a JSON string, and write the entire string to...
Summary of the BCO fields that are missing or incomplete: - provenance_domain - review - derived_from - obsolete_after - embargo - contributors (affiliation, email, orcid) - license - usability_domain -...
The BCO standard includes an "etag" field which should be a SHA256 of the BCO manifest. The hash should ideally be "canonical", which in this context means that it shouldn't...
The BCO format supports [SHA1 checksums for URI objects](https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/2791object.json?ref_type=heads#L42-46). These checksums are particularly useful for intermediate output files since they are usually deleted once the run completes. There is a...
The `accelerator` directive is currently supported for AWS Batch, Google Batch, and Kubernetes. Azure Batch also has GPUs, so this directive should also work for Azure Batch. Not sure yet...
It should be possible to generate a "stub" script from the process outputs, since the purpose of the stub is essentially to generate some empty output files that match the...