Mike Lin
Mike Lin
Just scratching a holiday itch....the `input:` heading in call bodies is useless clutter AFAICT. Make it optional (for backwards compatibility). Perhaps the idea was for call bodies to have additional...
e.g. ``` ~{true='hello ~{name}' false='goodbye ~{name}' condition} ``` The WDL spec says the RHS of true= and false= "MUST be string literals", not 100% clear whether that includes interpolations.
- [ ] migrate setup.py/setup.cfg/pbr/etc. to `pyproject.toml` - [x] update pyre or migrate to mypy (tedious! can we make GPT-4 do most of this work?) - [x] migrate pylint/flake8/black to...
cf. https://aws.amazon.com/blogs/industries/new-tools-to-accelerate-workflow-migrations-to-aws-healthomics/
https://github.com/chanzuckerberg/miniwdl/blob/main/WDL/runtime/backend/singularity.py#L94-L105 The default singularity configuration makes very little scratch disk space available, so we mount /tmp and /var/tmp to locations inside the run directory. This provides a good out-of-the-box experience,...
If task creates a symlink to the absolute path of an input file, we reject any use of the symlink in the task outputs, even though it should be OK...
https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline/blob/70025d47d2aea47043effa63f4f5d619004c9c7c/tasks/Qc.wdl#L319
Hello sir, thank you for pygtail; I'd like to inquire whether the GPL license vs a more permissive one is up for discussion, to simplify the considerations for developers and...
Currently any assertion failure is surfaced as a generic Assert_failure; we often have enough information to do much better.