
# Instructions for use:
# 1. Open this script in a text editor or IDE. Support for BASH
#    syntax highlighting can be helpful.
# 2. Search or scan visually for '<' or '>' characters to find places where
#    user input (e.g. a filepath or column name) is required. These must be
#    replaced with your own values. E.g. <column name> -> 'patient_id'.
#    Failure to remove '<' or '>' may result in `No such File ...` errors
# 3. Search for 'FIXME' comments in the script, and respond as directed.
# 4. Remove all 'FIXME' comments from the script completely. Failure to do so
#    may result in 'Missing Option' errors
# 5. Adjust the arguments to the commands below to suit your data and metadata.
#    If your data is not identical to that in the replayed analysis,
#    changes may be required. (e.g. sample ids or rarefaction depth)
# 6. Optional: replace any filenames in this script that begin with 'XX' with
#    unique file names to ensure they are preserved. QIIME 2 saves all outputs
#    from all actions in this script to disk regardless of whether those
#    outputs were in the original collection of replayed results. The filenames
#    of "un-replayed" artifacts are prefixed with 'XX' so they may be easily
#    located. These names are not guaranteed to be unique, so 'XX_table.qza'
#    may be overwritten by another 'XX_table.qza' later in the script.
# 7. Activate your replay conda environment, and confirm you have installed all
#    plugins used by the script.
# 8. Run this script with `bash <path to this script>`, or copy-paste commands
#    into the terminal for a more interactive analysis.
# 9. Optional: to delete all results not required to produce the figures and
#    data used to generate this script, navigate to the directory in which you
#    ran the script and `rm XX*.qz*`