nf-core launch refactoring #264
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This pull request introduces 3 alerts when merging fab91b8 into 04caa8c - view on LGTM.com new alerts:
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sven1103
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Feb 7, 2019
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🎉 Thanks Phil, great job in refactoring and solving the cyclic dependency!
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Had a play - fixed the python 2 errors, so Travis should now pass. Also did a whole lot of refactoring as I went through the code trying to figure out how it works. Should be a little more consistent now, plus I've integrated a lot of my old code in to the new processes instead of them working in separate ways.
Final bit about typing broke stuff for pipelines without a
parameters.settings.jsonfile, so one (probably small) bug left that I know of:..will be to do with setting the defaults and needing to use a
rangeor something (which I don't want to do). But time for bed now.Note that I made a few potentially controversial changes, such as only saving non-default values to the
parameters.jsonfile used to run the pipeline. Plus one or two other things. Feel free to take up in the review :)Phil