chanzuckerberg / miniwdl

Workflow Description Language developer tools & local runner

chanzuckerberg/miniwdl Issues

`struct` with optional fields
Closed 3 months ago2
Unusual behavior of `Directory` types that are cast to `String` and then entered into an `Array[String]`
Closed 3 months ago2
`miniwdl check` (v1.11.0) fails with certain input orders of array types in calls to `transpose`
Closed 3 months ago
MyPy thinks `WDL._util.strip_leading_whitespace` is a `str` and not a function.
Closed 3 months ago
No such function: write_objects
Updated 3 months ago
Get an interactive shell in a container
Updated 3 months ago
PermissionError when running miniwdl with Docker Desktop on Linux
Updated 3 months ago3
[Question]: is runtime container as an array supportted?
Updated 4 months ago2
Copy of input directory into Miniwdl "work" ?
Updated 5 months ago
MiniWDL dedents the command section *after* substituting placeholders, which causes problems if substituted values contain newlines
Updated 6 months ago2
recognize interpolation nested in true= false=
Updated 6 months ago1
Cleaning up abandoned MiniWDL services
Updated 6 months ago
Docker service level logs ought to be logged at higher than debug level when something goes wrong
Updated 6 months ago
Expose statistics about additional resource usage from containers
Updated 6 months ago4
MiniWDL can't parse a brace-enclosed command section with a brace in it
Updated 6 months ago1
`--containall` in Singularity will result in operation not permitted inside a Kubernetes pod
Updated 7 months ago
modernize pyproject tooling
Updated 8 months ago
`miniwdl check` plugins
Updated 8 months ago
Array coerces to String in MiniWDL
Updated 8 months ago
Miniwdl does not work on ARM macs (e.g. M1)
Updated 8 months ago6
miniwdl check does not enforce parameter_meta requirements per spec
Updated 8 months ago
v1.1 spec regex parsing
Updated 9 months ago2
How to ensure miniwdl waits for docker container to be in "healthy" state before executing task?
Updated 10 months ago
Python `WDL` fetch _all_ parameter meta
Updated 10 months ago6
Error running run_self_test in Ubuntu
Updated a year ago1
Add extension point for `String` to `File` coercion
Updated a year ago
Make sudo podman configurable
Closed 2 years ago5
[singularity] provide opt-out for tmp mount
Updated a year ago
Singularity incorrect output path resolution
Closed a year ago2
collect_by_key change object type
Closed a year ago3
Quoted numbers are not allowed in JSON but probably should be
Updated a year ago1
Miniwdl zip should allow additional files for packaging
Closed a year ago
Struct import issue
Closed a year ago1
Expression placeholder options like `sep` don't work
Closed a year ago4
Comparison of optionals doesn't work
Closed a year ago
`WDL.Env.merge` can make shadowed bindings rise from the dead to haunt the living
Closed a year ago2
Can miniwdl work with private docker images?
Updated a year ago1
Roadmap for adding `runtime` `gpu` attribute and `hints`.
Updated a year ago3
Singularity invocation "run" vs "exec"
Closed a year ago4
Support PyYAML 5.4
Closed 2 years ago
Identify duplicate key in error message
Closed 2 years ago
task cannot output absolute symlink to input file
Updated 2 years ago
Feeding the output of one task into another
Closed 2 years ago2
post-task chown failed: {'Error': None, 'StatusCode': 123}
Updated 2 years ago2
Miniwdl fails on list with optional outputs even though select_all is used
Closed 2 years ago4
`bind source path does not exist` when running miniwdl in a docker container
Closed 2 years ago3
Zip URI imports locally in local WDL
Closed 2 years ago2
AWS credential are not passed to runnner
Updated 2 years ago1
Problem with progressive uploads interracting with call caching
Updated 2 years ago1
`miniwdl check` with non-standard `runtime` keys
Updated 2 years ago