Move out integration processes #597
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I think there a few more things we need to do here before merging, so we still have a working workflow... Mostly we need to either remove or rename some things so that we are not calling processes that the script does not know about. (The alternative would be to import the module, but I don't think that is the direction we want to go at this point).
integrate.nf
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Do you want to rename this while you are at it, since it isn't integration at all now?
integrate.nf
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| @@ -180,4 +129,3 @@ workflow { | |||
| // generate integration report | |||
| integration_report(integrate_harmony.out, file(integration_template)) | |||
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Probably want to rename this report, and we need to get rid of the integration process calls above here?
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Maybe just comment this out for now, since we also don't have the rmd yet?
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Yeah, I'm fine with just commenting out most of this. I just don't like the idea of merging in changes that by their nature break the workflow.
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and we need to get rid of the integration process calls above here?
Ah, I totally missed this 🙃. I blame my long 🦃 break. These lines are gone now!
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In actual response to your feedback here, I was wary about going too far here and making |
…TODOs where those updates are on likely deprecated code
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Apparently github felt this update was sufficiently different to call it a whole new file instead of a diff!
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Let me know what you think of this now! I made some changes to get |
Co-authored-by: Joshua Shapiro <[email protected]>
Closes #592
A little 🍬 to get the ball rolling! This PR does what it says.