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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

WDL call cache can end up with copies of input files (and steal the originals) when they pass through cached tasks

bug

wdl

Status: Open.

#5562 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

toil kill does not clean up Mesos job working directories in Batch Mode

Status: Open.

#5556 In DataBiosphere/toil;

· Guigzai opened on Jul 30, 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

Slurm batch system: RuntimeError: Unknown jobID, could not be converted

slurm

Status: Open.

#5553 In DataBiosphere/toil;

· CGuichard opened on Jul 10, 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

Replace Slurm Docker for Slurm tests with https://hub.docker.com/r/giovtorres/slurm-docker/

Status: Open.

#5550 In DataBiosphere/toil;

· adamnovak opened on Jul 6, 2026

Document submitting a multi-node job using MPI (MPIRequirement) via Toil

Status: Open.

#5546 In DataBiosphere/toil;

· kinow opened on Jun 28, 2026

Singularity images are duplicated

Status: Open.

#5545 In DataBiosphere/toil;

· CGuichard opened on Jun 25, 2026