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Add support to PJM scheduler

Status: Open.

#5582 In DataBiosphere/toil;

· kinow opened on Sep 21, 2026

9.5.0 regression: no way to use a batch system + auto generated job store location

cwl

slurm

Status: Open.

#5581 In DataBiosphere/toil;

· mr-c opened on Sep 16, 2026

Chaining doesn't account for walltime requirements

Status: Open.

#5578 In DataBiosphere/toil;

· adamnovak opened on Aug 31, 2026

Many HPC batch systems stopped working due to walltime in prepareSubmission signature

Status: Open.

#5577 In DataBiosphere/toil;

· adamnovak opened on Aug 31, 2026

Add lint instructions to CONTRIBUTING file

Status: Open.

#5572 In DataBiosphere/toil;

· adamnovak opened on Aug 21, 2026

CWL step input errors with valueFrom and loadContents: true

Status: Open.

#5568 In DataBiosphere/toil;

· CGuichard opened on Aug 19, 2026

WDL output files can be mis-organized in the output directory if they come via the call cache

Status: Open.

#5564 In DataBiosphere/toil;

· adamnovak opened on Aug 7, 2026

Make toil-cwl-runner --cachedir work without bypassing the file store

cwl

Status: Open.

#5563 In DataBiosphere/toil;

· adamnovak opened on Aug 6, 2026

CWL job output files can end up in non-shared directories and cannot move between nodes with --bypass-file-store

Status: Open.

#5559 In DataBiosphere/toil;

· adamnovak opened on Aug 3, 2026

Support a primary fast/local and secondary slow/remote per-job storage for running jobs of different sizes

cwl

enhancement

Status: Open.

#5558 In DataBiosphere/toil;

· adamnovak opened on Aug 3, 2026

Provide CWL users with useful and documented ways of getting at files generated during failing workflow or step runs

Status: Open.

#5554 In DataBiosphere/toil;

· adamnovak opened on Jul 16, 2026

src/toil/test/docs/scriptsTest.py::ToilDocumentationTest::testMultiplejobs2 test is flaky because log messages from jobs can be handled out of order

Status: Open.

#5552 In DataBiosphere/toil;

· adamnovak opened on Jul 7, 2026