rabix / cwl-format

A very opinionated code formatter for CWL

Rabix has grown up!

Reproducible Analyses for Bioinformatics is now a reality!

Please see

• Common Workflow Language (github) for the specfication that the language part of Rabix merged into.
• Rabix Composer for a visual editor for CWL workflows
• This list of executors/runners that can run workflows in CWL on anything from your laptop to your HPC to your cloud.

If you want to see the old documentation for the project please see here

cwl-format's Issues

Insert any missing requirements

After parsing document

• add missing requirements.
• take out extraneous requirements?

First line should be `#!/usr/bin/env cwl-runner`

As per https://github.com/common-workflow-library/bio-cwl-tools#tool-feature-requirements-

Installation fails with pip and the tarball

Hi
when I try to install cwlformat 2022.2.18 with pip from the tarball
it fails because the tarball does not contain the Readme.md file.
The same for the LICENSE file.

The cause could be that the Readme.md file as well as the LICENSE file are not listed in the MANIFEST.in

remove extraneous 'id' fields

Some CWL generators, like cwlgen, output map<> format but still retain the id in the map entry's values, even though the 'id' value is also the map key.

This should be stripped out.

Example: https://github.com/PMCC-BioinformaticsCore/janis-pipelines/blob/536f8181dd3edaa7339483cc28610e3acde5d105/janis_pipelines/wgs_germline/cwl/WGSGermlineMultiCallers.cwl#L22

inputs:
  align_and_sort_sortsam_tmpDir:
    id: align_and_sort_sortsam_tmpDir
    doc: Undocumented option
    type: string
    default: ./tmp

Add an inline modification mode

I am happy to contribute this as well, if no one else wants to

How can I avoid removing comments in CWL ?

Hi,
while formatting CWL code, the cwl-format will remove all comment lines.
Can I avoid that somehow? I would like to have some comments in the code.
Is there a reason for removing comments by default?

Thanks,
Aleksandar

New release to fix ruamel.yaml incompatibility?

I would make the release myself, but I lack the permissions. Perhaps we could move this repository to https://github.com/common-workflow-lab/ for community maintenance?

How to convert a packed CWL workflow to a "normal" workflow supported by Rabix composer

If I use the cwltool --pack command, I will get a CWL document that contains the $graph key, but Rabix composer does not support this type of CWL document. How do I convert a CWL document that contains the $graph key into a "normal" CWL document?

importlib.resources breaks Python <3.7

I updated cwlformat today and noticed that importlib.resources breaks Python < 3.7 which won't work. I tried installed importlib-metada but this also doesn't work.

Just wondering if there are potentially any suggestions? I'm happy to PR convert keyorder.yaml into a Python files so it can be imported and used.

order of class and cwlVersion inconsitent with bio-cwl-tools recommendations

The contribution guide for bio-cwl-tools states that tools should start with:

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

The order done by cwl-format puts class first. While neither cwl-format nor bio-cwl-tools are formal standards, I'd suggest that cwl-format be changed to put cwlVersion first.

Peter

always convert to the shortest map<> variant

Would you accept a PR to add this?

Release for Python 3.6

Hi, I issued a PR (#5) for fixing Python 3.6. Just wondering if there's a release planned for this, or if there's something else that it's waiting on.

please tag a release

This is listed as a dependency for the latest version of benten, so a conda package will need to be built for cwlformat. However there is no release tagged - please tag a release to make it easier to build a conda package.

Thanks.

How can I get cwlformat to work on Py3.5

There is an error in cwl-format.

(env) ngsap2@ubuntu:~/cwl-format$ cwl-format /home/ngsap2/alignmentDocker.cwl > alignmentNewDocker.cwl
Traceback (most recent call last):
  File "/home/ngsap2/.local/bin/cwl-format", line 7, in <module>
    from cwlformat.formatter import main
  File "/home/ngsap2/.local/lib/python3.5/site-packages/cwlformat/formatter.py", line 105
    description=f"Rabix/cwl-format v{__version__}\n"
                                                   ^
SyntaxError: invalid syntax

Avoid JS engine use in string concatenation if possible

From common-workflow-lab/wdl-cwl-translator#127

Whenever something like the following appears: glob: $(inputs.outputVcf + ".tbi") cwl-format could replace it by glob: $(inputs.outputVcf).tbi