Updated to 3.1.0. Added automatic phyloseq R object creation for all datasets, including subsets if -s is specified. Waterway also can now create .tsv files for use with LEFse, which can be set in optional_analyses.txt. The level-x.csv file must first be downloaded from taxa-bar-plots.qza. Multiple bugfixes to the new R scripts, including filepath updates and script corner case management.

Hid the new files from the main waterway file, so they'll be added but wont be sourced yet. Added the framework for new R scripts to be run in the optional analyses block.

Update to 3.0.0. The major addition is the ability to filter the main dataset into sub-datasets called subsets through use of the -s command. waterway can recognize all subsets and run all analyses on either only the main dataset, or on all subsets as well.

Updated to 2.11.0, which includes major speed increases for the ANCOM block, removal of the make_collapsed_table option in config.txt, and changes to unran analyses messages.

Updated to 2.9, mostly a long needed code cleanup and partition for me. Code has been majorly broken up into smaller chunks, instead of one huge script (which was impossible for me to maintain after a while). The smaller chunks of code are located in the src folder, and are called by the master file waterway.bash. Smaller chunks of code being edited at a time is easier for me to maintain in the long run and can be more efficient, as the same chunk of code can be called multiple times under different decision trees. All variables are passed from waterway.bash to the code chunk and vice versa. Also moved some of the other help files into their own folder.

Removed reliance on python to generate manifest file. Manifest file generation is now written in bash, like everything else. Fixed some echo messages color.