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Setting up where Toil puts things is confusing

cwl

intern

wdl

Status: Open.

#5516 In DataBiosphere/toil;

· unito-bot opened on May 7, 2026

Support CPU and GPU-specific QOS options in Slurm batch system

Status: Open.

#5513 In DataBiosphere/toil;

· ctriquet-cs opened on May 6, 2026

Retry when Docker has internal timeouts behind MiniWDL

Status: Open.

#5511 In DataBiosphere/toil;

· adamnovak opened on May 4, 2026

README does not provide an obvious link to the right citation, or a machine-readable version of it

Status: Open.

#5509 In DataBiosphere/toil;

· kinow opened on May 1, 2026

Add the deprecation warnings to Google provisioner

Status: Open.

#5506 In DataBiosphere/toil;

· unito-bot opened on Apr 30, 2026

pytest import fails if kubeconfig has invalid OIDC token

Status: Open.

#5505 In DataBiosphere/toil;

· avnig05 opened on Apr 29, 2026

Toil should recognize when workflows not run by TRS ID have a TRS ID assigned, and associate it woth the workflow

Status: Open.

#5504 In DataBiosphere/toil;

· adamnovak opened on Apr 29, 2026

DRY: use sphinxcontrib-autoprogram to not repeat CLI option help text

good first issue

intern

Status: Open.

#5503 In DataBiosphere/toil;

· mr-c opened on Apr 27, 2026

src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_cancel_before_setup fails on Python below 3.14

Status: Open.

#5501 In DataBiosphere/toil;

· adamnovak opened on Apr 22, 2026

src/toil/test/utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory is flaky and can fail when a container cannot be created

Status: Open.

#5490 In DataBiosphere/toil;

· adamnovak opened on Apr 13, 2026

Update the Toil web site to avoid an externally managed environment error on install

intern

Status: Open.

#5488 In DataBiosphere/toil;

· unito-bot opened on Apr 10, 2026

Toil should add a pipx install bin to its own PATH

intern

Status: Open.

#5487 In DataBiosphere/toil;

· unito-bot opened on Apr 10, 2026