Issues

• Add support to PJM scheduler

  DataBiosphere/toil#5582 · Filter by author kinow opened on Sep 21, 2026
  2

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

  cwlslurm
  DataBiosphere/toil#5581 · Filter by author mr-c opened on Sep 16, 2026
  4

• Chaining doesn't account for walltime requirements

  DataBiosphere/toil#5578 · Filter by author adamnovak opened on Aug 31, 2026

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

  DataBiosphere/toil#5577 · Filter by author adamnovak opened on Aug 31, 2026

• Add lint instructions to CONTRIBUTING file

  DataBiosphere/toil#5572 · Filter by author adamnovak opened on Aug 21, 2026
  

• CWL step input errors with valueFrom and loadContents: true

  DataBiosphere/toil#5568 · Filter by author CGuichard opened on Aug 19, 2026

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

  DataBiosphere/toil#5564 · Filter by author adamnovak opened on Aug 7, 2026
  1

  

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

  cwl
  DataBiosphere/toil#5563 · Filter by author 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

  DataBiosphere/toil#5559 · Filter by author adamnovak opened on Aug 3, 2026
  1

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

  cwlenhancement
  DataBiosphere/toil#5558 · Filter by author 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

  DataBiosphere/toil#5554 · Filter by author 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

  DataBiosphere/toil#5552 · Filter by author adamnovak opened on Jul 7, 2026
  1

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

  DataBiosphere/toil#5550 · Filter by author adamnovak opened on Jul 6, 2026
  1

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

  DataBiosphere/toil#5546 · Filter by author kinow opened on Jun 28, 2026
  2

• Singularity images are duplicated

  DataBiosphere/toil#5545 · Filter by author CGuichard opened on Jun 25, 2026
  3

  

• --cwl-min-ram help is confusing: make us add Toil overhead

  cwlintern
  DataBiosphere/toil#5535 · Filter by author adamnovak opened on Jun 9, 2026

• Don't count image pulls towards CWL ToolTimeLimit

  cwl
  DataBiosphere/toil#5533 · Filter by author adamnovak opened on Jun 4, 2026

• Make Toil set CWL_SINGULARITY_CACHE if not set for CWL workflows

  cwlintern
  DataBiosphere/toil#5532 · Filter by author adamnovak opened on Jun 4, 2026

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

  cwlintern
  DataBiosphere/toil#5531 · Filter by author adamnovak opened on Jun 3, 2026

• Improve MiniWDL WDL 1.2 support

  internwdl
  DataBiosphere/toil#5527 · Filter by author unito-bot opened on May 29, 2026

• Setting up where Toil puts things is confusing

  cwlinternwdl
  DataBiosphere/toil#5516 · Filter by author unito-bot opened on May 7, 2026
  2

  

• Retry when Docker has internal timeouts behind MiniWDL

  DataBiosphere/toil#5511 · Filter by author adamnovak opened on May 4, 2026

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

  DataBiosphere/toil#5509 · Filter by author kinow opened on May 1, 2026
  2

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

  DataBiosphere/toil#5504 · Filter by author adamnovak opened on Apr 29, 2026

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

  good first issueintern
  DataBiosphere/toil#5503 · Filter by author mr-c opened on Apr 27, 2026
  1