cwltool

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Added make info at the end of the documentation related to useful make commands when developing for cwltool. Please check if the description is correct as I am not too...

jjkoehorst

Implementation of store RDF export of the workflow in CWL Prov RO-Bundle

15

Keeping as draft while we test proposed enhancements to CWLProv Added file size to prov RO-Bundle Creates a workflow.ttl file in the default folder while running. Then closes the file...

jjkoehorst

Evaluate requirements and hints using the correct input reference

11

Similar to #1566, with a tentative fix for the infamous #1330 :cowboy_hat_face: Letting CI run to see what breaks after the fix, before adding tests or making further changes. If...

kinow

improve test running on mac-os

4

@jfennick can you test this as well?

mr-c

Fixed another symlinking issue with Docker + staged files from InitialWorkDirRequirement

5

After two weeks of debugging, I think I finally fixed some additional symlinking issues. I will attempt to add a minimal example and/or tests soon, and failing that I will...

jfennick

fix empty scatter bug

1

fixes #1668 - [x] tests ~~why did no conformance test trigger this?~~ Scatter inputs in CWL v1.[012] must be arrays, not empty; so allowing this requires a change to the...

mr-c

Scatter before a when occurs

2

## Expected Behavior We are using a when to check if a variable is given to a workflow or not to execute a specific step. When this variable (a String[])...

jjkoehorst

CWLProv: cannot reproduce workflow runs with Directory input

2

**cwltool version: 3.1.20220628170238** Ran [this workflow](https://github.com/RenskeW/cwlprov-provenance/tree/f5dd87a950eeaf7f96bd39dc218164832ff3cbea/prov_data_annotations/example2) by @RenskeW with: ```console $ cwltool --provenance ro wf.cwl wf_job.yml ``` Then I tried reproducing the run and I got this error: ```console $...

simleo

Tasks for CWLProv

1

- [x] `make diff_pylint_report` is clean - [ ] Test with `toil-cwl-runner`, does this break anything? - [ ] move extra Python dependencies to an extra, add code to remind...

FarahZKhan

CWLProv cached runs

1

## Expected Behavior Able to distinguish the start time stamp in the provenance file of a workflow that was from a failed cache run and a succeeded run. ## Actual...

jjkoehorst