# Required initial parameters
samplesheet: "manifest.csv" # directions to the manifest for qiime import relative to this file
metadata: "metadata.txt"
base_name: "base_name_dataset" # name that will appear in the output file naming
input_type: "SampleData[PairedEndSequencesWithQuality]" # input type for qiime import
input_format: "PairedEndFastqManifestPhred33" # input format for qiime import
trim_forward: "GTGCCAGCMGCCGCGGTAA" # primer
trim_reverse: "GGACTACHVGGGTWTCTAAT" # primer

# Required parameters updated based on data
# End of Part 1
trunc_forward: "" # position to truncate forward reads in qiime dada2
trunc_reverse: "" # position to truncate reverse reads in qiime dada2
max: "" # maximum value alpha rarefaction plot

# End of Part 2
linkage_table: /path/to/file.txt # txt file obtained from database after uploading .rds file

# End of Part 3 
sampling_depth: "" # sampling depth for alpha rarefaction