3 ms·

> I don't think that a single one of these was meant to be used by wetlab biologists Speaking for myself, we didn't target wetlab biologists with WDL but we di

> I don't think that a single one of these was meant to be used by wetlab biologists Speaking for myself, we didn't target wetlab biologists with WDL but we did target "non-programmers" as MontyCarloHall described. This was influenced by the groups from which the original developers originated prior to working on the DSL. The degree to which we were successful can be debated, but hey that was the idea at least ;)

epistasis 5y ago
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-bioinformatics/ 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.
- geoffjentry 5y ago
  > 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.

3 ms·

> I don't think that a single one of these was meant to be used by wetlab biologists Speaking for myself, we didn't target wetlab biologists with WDL but we di

by geoffjentry 5y ago

epistasis 5y ago
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-bioinformatics/ 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.
- geoffjentry 5y ago
  > 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.