ebolyen
November 29, 2017, 11:09pm
3
Hey @nick-youngblut !
nick-youngblut:
If there are many sequencing runs (eg., dozens for the dataset that I’m working on), the iterative merging leads to a lot of redundant qiime feature-table merge commands, or a somewhat complicated bash script to handle a dynamic number of feature tables to iteratively merge.
Most definitely! This has been a pain-point we've been pretty unhappy with and we are currently working on what's needed to avoid it.
If only that was true
Here's some PRs I'm working on to enable variadic input if you want to keep up to date with the latest progress:
qiime2:master ← ebolyen:collection
opened 06:29PM - 09 Nov 17 UTC
`Set` and `List` are no longer primitive types, they are collection types. This
…
means they can be used on primitives (with the exception of metadata) or
semantic types. This enables variadic input artifacts in the framework.
~~**This is still under-tested. I'm going to be making changes to the CLI to make sure this works before returning to this PR**~~
https://github.com/qiime2/q2view/pull/81
qiime2:master ← ebolyen:collections
opened 07:29PM - 29 Nov 17 UTC
That doesn't get into actually allow feature-table merge to accept multiple inputs, but once these PRs are merged we'll be able to get started on that!
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