Mike Lin

@giuliovn Sorry again for my great delay in looking at this PR, I finally have some bandwidth opening for miniwdl maintenance again. How would you weigh adding this functionality against...

colima might even support docker swarm!? https://github.com/abiosoft/colima/discussions/469

Nuts- sounds like M3 processor or higher is needed for nested virtualization: https://github.com/douglascamata/setup-docker-macos-action/issues/35

@vtrifonov-altos The released Geneformer embeddings for 2024-07 were generated using a not-then-quite-final version of the [gf-12L-95M-i4096_MTLCellClassifier_CELLxGENE_240522](https://huggingface.co/ctheodoris/Geneformer/tree/main/fine_tuned_models/gf-12L-95M-i4096_MTLCellClassifier_CELLxGENE_240522) model fine-tuned by the Geneformer authors themselves. It was shortly before they released that...

@staksh Sorry that `[downloads_awscli]` option only applies to the synthetic S3 downloader tasks. The [`[task_runtime] env`](https://github.com/chanzuckerberg/miniwdl/blob/5d35e53240ac62ba1b0f30910eedace102256d18/WDL/runtime/config_templates/default.cfg#L138-L145) option might help for arbitrary tasks, I think something like ``` [task_runtime] env =...

@stxue1 It should work of you omit the `glob.` prefix from the input keys. I agree it should tolerate that prefix though.

@multimeric I don't think the WDL spec calls for the desired type narrowing, and instead has several examples along the lines of `if defined(optional) then ... select_first([optional]) ... else ...`....

@multimeric I like this, but are we sure it's okay with the parentheses? Does the path need to be absolute or relative to any particular directory?

Yea where [`SubprocessBase` formulates `cli_log_filename`](https://github.com/chanzuckerberg/miniwdl/blob/6ecfc6f622a38588c2b6d34c849140ae8e6c9971/WDL/runtime/backend/cli_subprocess.py#L70) it should incorporate its base class' `TaskContainer.try_counter` similarly to how [it's used in the std{out,err}.txt filenames](https://github.com/chanzuckerberg/miniwdl/blob/6ecfc6f622a38588c2b6d34c849140ae8e6c9971/WDL/runtime/task_container.py#L472-L480).

@brianraymor if you'd like to take an early look and verify the line-level diff: https://github.com/chanzuckerberg/cellxgene-census/pull/1433/commits/daa1638116249bbefb054493fbea00cae38c88b6 (I've launched a test build with these changes 🤞 )