Sphesihle Makhathini

fileJobStore needs to handle arbitrary (or permission denied) os.link errors to work on some filesystems

5

I'm trying to run this simple workflow. **cwltoil version**: 3.15.0 **cwltool version**: 1.0.20180525185854 cwlfile [touchfile.cwl] ``` cwlVersion: v1.0 class: CommandLineTool baseCommand: touch hints: DockerRequirement: dockerPull: ubuntu:18.04 arguments: - output-$(inputs.num).txt inputs:...

parse commandline flags/options when validating workflow

2

I have a workflow that uses a cwl-extension which is not part of the standard. I'd like to be able to parse the "--enable-ext" flag to cwltool when validating the...

Saving recipe information for a future run

1

Here is the code for the previous attempt at this https://github.com/ratt-ru/Stimela/blob/38d11d628954e868e30cca3663dbcfea424279a1/stimela/recipe.py#L612-L641

cab specification 2.0

38

The cab specification has a few obvious flaws. These ones are particularly bad: * does not distinguish between files and directories * does not allow a pattern specification (pinging @bennahugo...

With things becoming easier to install these days, we should allow users to use stimela with applications on their machines.

Add unit tests for cabs

2

Every Cab should have a test.py file which does the following: - Tests basic run with default parameters - A failure test to see if it reports an exception if...