Alex Kanitz

Semantics of error states ambiguous

2

### Description of the problem Running different WES implementations, we ran into the issue that the definition of state `EXECUTOR_ERROR` is somewhat ambiguous. The relevant states are [currently defined](https://github.com/ga4gh/workflow-execution-service-schemas/blob/c3b19854240c4fcbaf3483e22b19db0a918a7ee5/openapi/components/schemas/State.yaml#L27-L34) as:...

Pass TES endpoints to WES request

2

For WES implementations that support TES (e.g. [cwl-WES](https://github.com/elixir-cloud-aai/cwl-WES)), there is currently not an mechanism to provide a list of acceptable TES endpoints, requiring TES endpoints themselves or a mechanism to...

Support passing TRS URIs to workflow_url

4

#### Current situation Similar to DRS URIs, [TRS URIs](https://ga4gh.github.io/tool-registry-service-schemas/DataModel/) have been proposed to be used as unique identifiers for resources on TRS services, which may include workflows (note the [open...

No tag/release for version 1.0.1

4

The [reference documentation](https://ga4gh.github.io/workflow-execution-service-schemas/docs/) linked to in this repository's `README.md` is for version `1.0.1` of the specification. However, there is no corresponding [release](https://github.com/ga4gh/workflow-execution-service-schemas/releases) and/or [tag](https://github.com/ga4gh/workflow-execution-service-schemas/tags) for version `1.0.1` (latest tag and...

Default branch & release model

4

Before the WES API was officially adopted by the GA4GH, it was voted that the `develop` branch should be the default branch for WES (and other Cloud APIs) for reasons...

It would be nice to have a reference documentation for each API release rather than only having a single documentation version that points to the latest release (or, as it...

Type inference for Flask app object wrong in VS Code

2

### Description When creating a `FlaskApp` with connexion, the type information for the wrapped Flask app object is inferred wrong by VS Code with Pylance. While I do understand that...

Logger config overrides client logger config

6

### Problem When importing `genomepy` before setting a host application's `logger` config, `genomepy`'s logging configuration is used instead. Similar issues in other packages: - https://stackoverflow.com/questions/66747718/overriding-a-third-party-modules-logger - https://github.com/pytorch/pytorch/issues/85952 ### To reproduce...

## Problem We have run into a problem that suggest that in certain situations, Funnel may return a task ID to the client before a database document for the task...

Add `.snakemake-workflow-catalog.yml` file for configuring usage instructions for the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog) Fixes #151