interconvertibility between workflow languages and wdl

[robertchasechanning]

I think some updates would be helpful in keeping this repo relevant and a good source of information.

• Adding a section on cwl.

The debate about which workflow language to use may actually prevent adoption of the structured workflow paradigm in organizations where people do not want to invest years of programming into technologies which will be deprecated.. This fear of failure can be resolved by mentioning that the workflow languages are interconvertible.

• Adding a section about the interconvertibility of the different worfklow systems
• Snakemake can be converted to cwl using the --export-cwl directive [1]
• cwl can be converted to nextflow using cwl2nxf-*.jar [2]
• cwl can be converted to wdl [3,a 3ai]
• wdl can be converted to cwl [4a, 4b]

[1] https://snakemake.readthedocs.io/en/stable/executing/interoperability.html# [2] https://www.nextflow.io/blog/2017/nextflow-and-cwl.html [3a] https://github.com/adamstruck/cwl2wdl [3ai] https://bioconda.github.io/recipes/cwl2wdl/README.html [4a] https://github.com/common-workflow-lab/wdl-cwl-translator [4b] https://github.com/common-workflow-lab/wdl2cwl

[grst]

Thanks for your input! However, I believe this repo is now obsolete in favor of the excellent review paper by Wratten et al and the associated example repository. I should probably archive it.