DataBiosphere toil issues

DataBiosphere / toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

http://toil.ucsc-cgl.org/.

Apache License 2.0

878 stars 237 forks source link

issues

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Update Toil Phoenix tutorial

#4991 unito-bot opened 1 hour ago
0
Prevent simultaneous pulls of Singularity images by toil-cwl-runner: add locking

#4990 unito-bot opened 1 day ago
0
Bump mypy from 1.10.0 to 1.10.1

#4989 dependabot[bot] closed 1 day ago
0
Defer file virtualization until use for WDL String-to-File coercion

#4988 stxue1 opened 1 day ago
0
Move/write list_multipart_uploads to its own library file and add a test.

#4987 DailyDreaming opened 1 day ago
0
Move/write head_s3_object to its own library file and add a test.

#4986 DailyDreaming opened 1 day ago
0
Move/write delete_iam_instance_profile to its own library file and add a test.

#4985 DailyDreaming opened 1 day ago
0
Move/write delete_iam_role to its own library file and add a test.

#4984 DailyDreaming opened 1 day ago
0
Removing whitespace in WDL doesn't work for overindented code blocks

#4983 stxue1 opened 4 days ago
3
Support inputs for task only WDLs, pass through task exit codes, and respect explicit null inputs

#4982 stxue1 opened 4 days ago
0
Respect user supplied null values for workflow/task inputs

#4981 stxue1 opened 4 days ago
0
Integration test fixes.

#4980 DailyDreaming opened 6 days ago
0
Update psutil requirement from <6,>=3.0.1 to >=3.0.1,<7

#4979 dependabot[bot] closed 1 week ago
0
Return workflow exit code for toil-wdl-runner

#4978 stxue1 opened 1 week ago
0
Allow user to supply inputs to singleton task WDL workflows

#4977 stxue1 opened 1 week ago
0
Add toil debug-job tutorial

#4976 adamnovak closed 1 day ago
0
Allow for not installing the mypy_boto3_* packages

#4975 mr-c opened 1 week ago
0
Investigate and fix failing CI on Toil master branch

#4974 unito-bot closed 1 day ago
2
Handle permanent EIOs in file locking by eventually stopping

#4973 adamnovak opened 1 week ago
0
Toil can hang when something goes wrong with file locking on Ceph

#4972 adamnovak opened 1 week ago
1
toil-cwl-runner used to allow `--defaultMemory 0`, which has special meaning to Slurm, but now no longer does

#4971 gmloose opened 1 week ago
2
Make backports.zoneinfo a normal dependency

#4970 adamnovak closed 6 days ago
0
Missing non-dev dependency on `backports.zoneinfo`

#4969 adamnovak closed 6 days ago
0
Make WDL errors and container dumps trace where files came from

#4968 unito-bot opened 2 weeks ago
0
Update google-cloud-storage requirement from <=2.8.0,>=2 to >=2,<=2.17.0

#4967 dependabot[bot] closed 2 weeks ago
1
Update kubernetes requirement from <22,>=12.0.1 to >=12.0.1,<31

#4966 dependabot[bot] closed 2 weeks ago
1
Fix bad caching to prevent already devirtualized files getting lost

#4965 stxue1 closed 2 weeks ago
0
Re-enable failing on warnings in the docs build

#4964 adamnovak closed 2 weeks ago
0
The CWL integration tests fail when they land on the Toil gitlab runners and pass on the shared ones

#4963 adamnovak closed 3 weeks ago
2
Change pinned htcondor versions to fix CI

#4962 stxue1 closed 3 weeks ago
0
CI breaking since some htcondor versions are gone

#4961 stxue1 closed 3 weeks ago
0
Support running singleton WDL tasks

#4960 stxue1 closed 2 weeks ago
0
Virtualized file not found in toil-wdl-runner when multiple stdout() calls in output "collide"

#4959 stxue1 closed 2 weeks ago
0
Add `--printStatus` to documentation + Fix message bus path getting lost

#4958 stxue1 closed 3 weeks ago
0
Update requests requirement from <=2.31.0 to <=2.32.3

#4957 dependabot[bot] closed 3 weeks ago
2
Dry run support in toil-wdl-runner

#4956 unito-bot opened 4 weeks ago
1
Make Gitlab not drop off the Internet for no reason

#4955 unito-bot closed 1 day ago
1
Print hash with --version when installed as development

#4954 stxue1 closed 3 weeks ago
1
Allow Toil utils to work without the AWS extra

#4953 stxue1 closed 3 weeks ago
0
Toil utils do not work if AWS libraries are not installed

#4952 stxue1 closed 3 weeks ago
0
Grab GPU partition information from Slurm + Support for `gpu` field in WDL

#4951 stxue1 closed 2 weeks ago
4
Better logs when accessing large files from S3

#4950 adamnovak closed 3 weeks ago
0
Support WDL 1.1 standard `gpu: true` Runtime attribute

#4949 adamnovak closed 2 weeks ago
0
Support running a single WDL task instead of a whole workflow

#4948 unito-bot closed 2 weeks ago
0
Make Slurm logging quieter

#4947 adamnovak closed 3 weeks ago
0
`toil debug-job --help` prints automatic default option values where `toil-wdl-runner --help` does not for the same option

#4946 adamnovak opened 1 month ago
0
Add an argument to specify number of GPUs to use for a `toil-wdl-runner` task

#4945 stxue1 opened 1 month ago
1
Update setuptools requirement from <70,>=65.5.1 to >=65.5.1,<71

#4944 dependabot[bot] closed 1 month ago
0
Update requests requirement from <=2.31.0 to <=2.32.2

#4943 dependabot[bot] closed 1 month ago
1
Replace all the _OVERRIDE environment variables with options on toil debug-job

#4942 unito-bot opened 1 month ago
0