Overall name changes

[cjfields]

I'm readying some code for possibly working on a DSL2 port at some point, which also includes renaming some of the process names and moving R code into template files; the start of this is on the dev branch. This will affect config files, though at some point we should think about a good base config to store everything in.

[cjfields]

Changing task name to indicate breaking changes

[cjfields]

@grbot I have some fairly significant changes in a branch feature/se-analysis (from dev) that allows (optional, off by default) separate processing of R1 and R2. This need popped up recently with some V3-V4 analyses we have, where the quality of reads at the ends is causing issues with merging. This is also a (surreptitious) lead up to incorporating SE read processing, including 454, etc. I'll likely work on this a bit more to make it more flexible, but will eventually merge it into the dev branch.

The reason I mention all of this: during this work I also made file names a bit more consistent based on whether the analysis is performed on the merged reads, R1, or R2, and whether we are renaming the taxa IDs using MD5 or a simple ('ASV1') naming scheme. This might break some scripts that expect a specific name; I'll try documenting these a bit more in detail prior to merge in case there are any questions.

[cjfields]

Also, I am very seriously considering re-organizing the output directories, but will do this in a separate branch once these changes are merged in.