Issues · DataBiosphere/toil · GitHub

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Setting up where Toil puts things is confusing

#5516

· unito-bot opened

on May 7, 2026

Retry when Docker has internal timeouts behind MiniWDL

#5511

· adamnovak opened

on May 4, 2026

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

#5509

· 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

#5504

· adamnovak opened

on Apr 29, 2026

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

good first issue

#5503

· mr-c opened

on Apr 27, 2026

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

#5501

· 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

#5490

· adamnovak opened

on Apr 13, 2026

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

#5488

· unito-bot opened

on Apr 10, 2026

Toil should add a pipx install bin to its own PATH

#5487

· unito-bot opened

on Apr 10, 2026

Tests that need multiple CPU cores don't know how many CPU cores they need to pass, and can fail when the system has too few

#5482

· sanvila opened

on Mar 31, 2026

Record CPU usage of Docker containers under CWL

#5477

· adamnovak opened

on Mar 24, 2026

`make test` can't run doctests because it captures output, but tries anyway

#5474

· adamnovak opened

on Mar 18, 2026