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Updating paths before first weld #43

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merged 12 commits into from
Aug 10, 2020

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@gwaybio gwaybio commented Aug 5, 2020

The recipe will be called as a submodule in the template repo. This pull request ensures that a call to bash weld.sh will call the versioned controlled recipe scripts.

An important note here is that after this is merged, testing with the recipe as we have in the past will no longer work.

A second important note is that the config_utils.py file will eventually be moved to the template (this way all the config related files are kept in one place). This is the current thinking right now at least.

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Doesn't really fit with the theme of this PR, but since it touches print() statements it made me think, it would be nice to have a print() at the end of every step saying it's done.
0./1. and 0./2. already end with print("All sites complete.") but something like print("Step 0./0. processing complete.") would be nice to have at the end of other steps.

@gwaybio gwaybio mentioned this pull request Aug 6, 2020
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gwaybio commented Aug 6, 2020

Awesome - agree with your suggestion (see #46 )

An important note here is that after this is merged, testing with the recipe as we have in the past will no longer work.

We really need to get some testing done in this repo 😖

I am thinking that I can address #45 here, if we can solve it quickly (should be a super quick fix once we settle on nomenclature)

this is still where the weld is broken, working through it now
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gwaybio commented Aug 10, 2020

Prepare for a landmark pull request merge! This PR represents the bulk of the remaining fixes to welding version 0.1 🎉

@gwaybio gwaybio merged commit 28c5b20 into broadinstitute:master Aug 10, 2020
@gwaybio gwaybio deleted the prep-for-first-weld branch August 10, 2020 20:08
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