Example WDL test for gpu's does not work depending on default executor container

[stxue1]

In the test_gpu_task.wdl example test, it depends on the lspci command from the default executor container as no container is specified.

For MiniWDL and Toil, the default container is Ubuntu 20.04:
https://github.com/chanzuckerberg/miniwdl/blob/a34aa902ec1be2f411db1e38daf51bae4f839f42/WDL/runtime/config_templates/default.cfg#L144-L146

But the base Ubuntu 20.04 doesn't support lspci:

$ docker run -it ubuntu:20.04 bash
root@d3b58db61322:/# lspci
bash: lspci: command not found

I think some container with lspci preinstalled should be specified. Ex:

FROM ubuntu:22.04

RUN apt-get -y update && apt-get -y install pciutils

and

  runtime {
    gpu: true
    container: "quay.io/stxue/ubuntu_lspci:latest"
  }

which allows the test to run:

stxue@mustard:/private/groups/patenlab/toil-dev/wdl-conformance-tests$ srun -c 1 --mem 1G --time=0:10:00 --partition gpu --gres=gpu:1 --pty bash -i
stxue@phoenix-05:/private/groups/patenlab/toil-dev/wdl-conformance-tests$ toil-wdl-runner test_gpu_task.wdl 
/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated and will be removed in a future release
  "class": algorithms.Blowfish,
[2024-05-29T13:39:17-0700] [MainThread] [I] [toil] Running Toil version 7.1.0a1-e9d0b62d7d62af9672946858fdd6fb587b1dd563 on host phoenix-05.prism.
/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated and will be removed in a future release
  "class": algorithms.Blowfish,
[2024-05-29T13:39:18-0700] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run
[2024-05-29T13:39:18-0700] [MainThread] [I] [toil.leader] Issued job 'WDLTaskJob' wf.test_gpu.command kind-WDLTaskJob/instance-52hhmugy v1 with job batch system ID: 2 and disk: 2.0 Gi, memor
y: 2.0 Gi, cores: 1, accelerators: [{'count': 1, 'kind': 'gpu'}], preemptible: False
/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated and will be removed in a future release
  "class": algorithms.Blowfish,
/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated and will be removed in a future release
  "class": algorithms.Blowfish,
[2024-05-29T13:39:25-0700] [MainThread] [I] [toil.leader] Finished toil run successfully.

Workflow Progress 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 (0 failures) [00:06<00:00, 0.48 jobs/s]
{"wf.out": true}
[2024-05-29T13:39:25-0700] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/data/tmp/tmpxfvwtsc1/tree)

stxue@phoenix-05:/private/groups/patenlab/toil-dev/wdl-conformance-tests$ MINIWDL__SCHEDULER__CONTAINER_BACKEND=singularity miniwdl run test_gpu_task.wdl 
2024-05-29 13:40:34.114 wdl.w:wf workflow start :: name: "wf", source: "test_gpu_task.wdl", line: 2, column: 1, dir: "/private/groups/patenlab/toil-dev/wdl-conformance-tests/20240529_134034_wf"
2024-05-29 13:40:34.118 wdl.w:wf miniwdl :: version: "v1.12.0", uname: "Linux phoenix-05.prism 5.15.0-78-generic #85-Ubuntu SMP Fri Jul 7 15:25:09 UTC 2023 x86_64"
2024-05-29 13:40:34.146 wdl.w:wf ready :: job: "call-test_gpu", callee: "test_gpu"
2024-05-29 13:40:34.147 wdl.w:wf.t:call-test_gpu task setup :: name: "test_gpu", source: "test_gpu_task.wdl", line: 9, column: 1, dir: "/private/groups/patenlab/toil-dev/wdl-conformance-tests/20240529_134034_wf/call-test_gpu", thread: 139860603147840
    0:00:00 elapsed    ▬▬▬        tasks finished: 0, ready: 1, running: 0/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated and will be removed in a future release
  "class": algorithms.Blowfish,
2024-05-29 13:40:34.369 wdl.w:wf.t:call-test_gpu Singularity runtime initialized (BETA) :: singularity_version: "singularity-ce version 3.10.3"
2024-05-29 13:40:34.377 wdl.w:wf.t:call-test_gpu singularity run :: pid: 3168507, log: "/private/groups/patenlab/toil-dev/wdl-conformance-tests/20240529_134034_wf/call-test_gpu/singularity.log.txt"
2024-05-29 13:40:34.651 wdl.w:wf.t:call-test_gpu done
2024-05-29 13:40:34.651 wdl.w:wf finish :: job: "call-test_gpu"
2024-05-29 13:40:34.652 wdl.w:wf done
{
  "dir": "/private/groups/patenlab/toil-dev/wdl-conformance-tests/20240529_134034_wf",
  "outputs": {
    "wf.out": true
  }
}