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Don't count image pulls towards CWL ToolTimeLimit

cwl

Status: Open.

#5533 In DataBiosphere/toil;

· adamnovak opened on Jun 4, 2026

Make Toil set CWL_SINGULARITY_CACHE if not set for CWL workflows

cwl

intern

Status: Open.

#5532 In DataBiosphere/toil;

· adamnovak opened on Jun 4, 2026

toil-cwl-runner should allow http://commonwl.org/cwltool# namespaced extensions by default

cwl

intern

Status: Open.

#5531 In DataBiosphere/toil;

· adamnovak opened on Jun 3, 2026

Improve MiniWDL WDL 1.2 support

intern

wdl

Status: Open.

#5527 In DataBiosphere/toil;

· unito-bot opened on May 29, 2026

src/toil/lib/encryption/_nacl.py::toil.lib.encryption._nacl.decrypt test is flaky

intern

Status: Open.

#5521 In DataBiosphere/toil;

· adamnovak opened on May 19, 2026

Setting up where Toil puts things is confusing

cwl

intern

wdl

Status: Open.

#5516 In DataBiosphere/toil;

· unito-bot opened on May 7, 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

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