General syntax

waterway should be run in the following format:

waterway [path_to_config.txt] [options]

Path to config.txt

When waterway is first run in a new location (or when you point it to a new location), it will automatically create config.txt and optional_analyses.txt. Ignore optional_analyses.txt when you first run it, and instead go into the config file and change all required parameters. Then, once the parameters are changed, run waterway and direct it to the folder containing config.txt and optional_analyses.txt. For example, if the config files were located at /home/michael/config1/config.txt, the command would be:

waterway /home/michael/config1

Options

IMPORTANT: When using options with waterway, you must enter the path to the directory containing the config files as the first argument.

waterway currently supports the following options:

-f    List the functions used in waterway, then exit.
-F    Run FastQC and MultiQC on the .fastq.gz files located at the filepath specified in config.txt.
-h    Show a brief overview of waterway and its options, then exit.
-l    Log all output to a log.out file created in the same folder as waterway.
-m    Use a manifest file for the import step, as specified in the sourcefile.
-M    Make a manifest file from the files located at the filepath.
      This assumes that the Sample_ID is all text located before the first underscore in the filename.
-n    Print the version number of this script, then exit.
-r    Replaces underscores with hyphens in patterns inputted into the forward/reverse patterns in config.txt.
      Useful for quickly fixing filename and SampleID errors when making a manifest file.
-s    Create subsets from filtered metadata files added to "filter_inputs".
-t    Tests the output status, then exit. Print the unfinished and finished steps for the data.
-T    Filter table.qza according to a filtered metadata file, located in the directory "filter_inputs".
      The directory is automatically created when running the option for the first time.
-v    Verbost output. Enables detailed output of the waterway workflow.


The following options install or enable commands, and should only be run once

--add-waterway       Adds the waterway command to ~/.bashrc
--install-deicode    Installs the DEICODE Qiime2 plugin
--install-picrust    Installs the Picrust2 Qiime2 plugin

The following shortform options are also available in longform for readability:

-c    --train-classifier
-f    --show-functions
-F    --fastqc
-h    --help
-l    --log
-m    --manifest
-M    --make-manifest
-n    --version
-r    --rename
-s    --subsets
-t    --test
-T    --filter-table
-v    --verbose

--install-deicode
--install-picrust

waterway supports multiple option inputs at once. To input options into waterway, use the general formula:

./waterway.bash {path_to_config.txt} (options here)

For example, when running waterway with with a manifest file import and logged output (and assuming the config files were located in the same place as the last example) the input would be:

./waterway.bash /home/michael/config1.txt -m -l

Take note that some options like -t or -f exit after completion (as specified above), and therefore will terminate waterway before other options are considered. These options should be run one at a time.