How to save workflows with steps from multiple directories?

[jvdzwaan]

I usually work with generic vs. project specific cwl steps that are loaded from different directories, for example https://github.com/WhatWorksWhenForWhom/nlppln and https://github.com/KBNLresearch/ochre. How to make sure workflows that use steps from multiple directories can be run on different computers?

Packed workflows may be the best solution.

This is issue is related to #25

[atzeus]

Using inline workflow. Currently we cannot remove the #!/usr/bin/env cwl-runner comments in the middle of the files. See https://bitbucket.org/ruamel/yaml/issues/31/provide-a-way-to-get-the-comment-string

[atzeus]

The inline files will get long id's and extra info, this is a bug in cwltool(?)

common-workflow-language/cwltool#564

[atzeus]

Works now (from commit b487ef5) by giving inline=True to save (default false). Issues mentioned above, may get resolved in later versions of ruamel and cwltool

[LourensVeen]

Fixed the shebang issue by digging into ruamel deeper, and the id's can be fixed by manually giving them local JSON-LD IRIs, so that cwltool doesn't add file:// IRIs. Both a bit ugly, but it worked (I added a test case too).