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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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Replace pipeline.ini files with pipeline.yml #10

Closed AndreasHeger closed 6 years ago

AndreasHeger commented 6 years ago

A basic converter has been added in script/cgat_ini2yml.py.

Next steps: Convert all ini files in the repository Convert all ini files in the test data sets Remove .ini parsing from CGATCore/Pipeline/Parameters.py

AndreasHeger commented 6 years ago

This relates to https://github.com/cgat-developers/cgat-core/issues/18

@sebastian-luna-valero - I will add a pipeline.yml file to the test data sets, keeping the pipeline.ini in place to minimize breakage.

AndreasHeger commented 6 years ago

Using yaml will break all "section_parameter" references. Might still be necessary to add a flattened hierarchy to limit refactoring. Will work on separate branches.

Acribbs commented 6 years ago

Thanks Andreas. Are we now using .format for all string substitution going forward?

AndreasHeger commented 6 years ago

TBH, I don't know. I have been using .format now because it seems to be more powerful for normal substitutions. However, the substitution of command line parameters in P.run() still relies on '%s' and maybe we should keep that to avoid rewriting every command.

Acribbs commented 6 years ago

In my own code I have been using .format too because I like the fact that you can change the positional arguments very easily. Ok, will stick to %s for pipeline statements

AndreasHeger commented 6 years ago

This has been done, see #11