stxue1

Figure out a way to run WDL and CWL runners without nondefault Docker privileges

2

We do some trickery with syscalls and whatnot to allow Singularity to run inside the container https://github.com/DataBiosphere/toil/blob/5d436d3b094dc3bec017a770c7fe04ce2f345267/src/toil/provisioners/abstractProvisioner.py#L820 This means `toil-wdl-runner` (and maybe `toil-cwl-runner`) is unable to run inside a default...

Add an argument to specify number of GPUs to use for a `toil-wdl-runner` task

1

WDL 1.1 says that tasks can be [specified to need GPUs](https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#gpu): > ```wdl > task gpu_test { > #..... > runtime { > gpu: true > } > } >...

On the Slurm cluster, where Toil is installed with only the WDL extra: ``` stxue@mustard:/private/groups/patenlab/toil-dev/wdl-conformance-tests$ toil --version /usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated "class": algorithms.Blowfish, Traceback (most recent call last):...

Spike: Determine work necessary to get rid of Docker in Docker

2

Docker in docker was originally made for Mesos, but most batchsystems nowaday are not as compatible with our current Docker in Docker configuration; there shouldn't be much reason to run...

This closes #4988 ## Changelog Entry To be copied to the [draft changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog) by merger: * toil-wdl-runner will not immediately error on nonexistent coerced files until outputted * `File?` type...

Closes #4995 ## Changelog Entry To be copied to the [draft changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog) by merger: * Support WDL disk specification as per 1.1 spec ## Reviewer Checklist * [ ] Make...

Support filename coercion back to string

1

The spec expects that filenames can be represented as a string to alter things like filename extensions: https://github.com/openwdl/wdl/blob/9c0b9cf4586508a9e6260cc5c5e562e21f625aac/SPEC.md?plain=1#L6521 We virtualize files into our own representation, so coercing back will give...

> If an array of disk specifications is used to specify multiple disk mounts, only one of them is allowed to omit the mount point. https://github.com/openwdl/wdl/blob/9c0b9cf4586508a9e6260cc5c5e562e21f625aac/SPEC.md?plain=1#L4336 We don't currently support...

```wdl version 1.1 workflow testWorkflow { input { } call testTask output { Array[File?] array_in_output = testTask.array_in_output Int len_in_output = testTask.len_in_output Array[File?] array_in_body_out = testTask.array_in_body_out Int len_in_body_out = testTask.len_in_body_out Array[File?]...

This is for behavioral parity with miniwdl. Related to https://github.com/openwdl/wdl/issues/667 ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1601) ┆Issue Number: TOIL-1601