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A comment on Amazon Genomics CLI. Parent comment

Re:Amazon Genomics CLI by epistasis on Saturday August 21, 2021 @12:31PM (#28258272)
Wetlands biologists tend to be pretty clever, and I have no more difficulty teaching them small bits of AWK to do some quick calculations on their laptop than I do new hires that are very skilled with Python.

If you look at a small WDL tutorial, such as this:

https://www.rc.virginia.edu/userinfo/howtos/rivanna/wdl-bioi...

I think that this is more complex than, say, defining Afro data types, as it involves calling tasks like functions, string substitutions, filling in variables from a config file, etc. There’s a certain base level of complexity that can be hard to abstract away, and I don’t think this has yet got to the simplicity of, say, pivot tables in Excel.

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Re:Amazon Genomics CLI by geoffjentry on Saturday August 21, 2021 @01:28PM (#28258804)
> There’s a certain base level of complexity that can be hard to abstract away

100% and a conclusion I came to far too long into my tenure in the bioinformatics workflow domain. It is also why I soured a bit on some of the GA4GH efforts in the same space (WES & TES in particular).

I still very much agree w/ the goals & ideals (respectively), but in my experience the middle ground between "I don't care, just give me the defaults" and "please do not abstract away any of the complexity, I need that" is quite small. And that zone would be the sweet spot for these efforts.

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