IMPORTANT: For all paths in config.txt, make sure that you note whether it ends with a trailing slash (/) or not, and preserve this when inputting your paths.
projpath –> The path to the directory containing three subdirectories: one with the raw fastq files, one with the metadata, and an output folder.
filepath –> The path to the directory containing the raw fastq files.
qzaoutput –> The path to the directory that will contain all output files. If rerunning analysis, this should point to the directory containing all previously outputted files.
metadata_filepath –> The path to the metadata file, as a tab-separated value (.tsv) file.
manifest –> The path to your manifest file, as a tab-separated value (.tsv) file.
manifest_format –> The format of your files, as inputted into the qiime2 “qiime tools import” command.
trimF –> The nucleotide which to cut until from the start of the read, for all forward reads.
trimR –> The nucleotide which to cut until from the start of the read, for all reverse reads.
truncF –> The nucleotide which to cut until from the end of the read, for all forward reads. Formatted as an array, so you can try out multiple trunc points. For multiple trunc points, format the variable as (trunc1 trunc2 trunc3 …). Note that every combination of truncF/truncR will be tried.
truncR –> The nucleotide which to cut until from the end of the read, for all reverse reads. Formatted as an array, so you can try out multiple trunc points. For multiple trunc points, format the variable as (trunc1 trunc2 trunc3 …). Note that every combination of truncF/truncR will be tried.
sampling_depth –> The sampling depth as used in the qiime2 “qiime diversity core-metrics-phylogenetic” command.
beta_diversity_group –> The group column to compare within when measuring beta diversity. Must be inputted exactly as written in the metadata file (caps sensitive).
classifierpath –> The path to the trained classifier file
download_greengenes_files_for_me –> Set to “true” for automatic greengenes database files download.
greengenes_path –> Optional variable. Path to existing greengenes database files (if they exist). Classifier is also saved here instead.
forward_primer –> The forward primer used during library prep.
reverse_primer –> The reverse primer used during library prep. Combines with forward_primer to extract sequences between these primers in 16S.
min_read_length –> The minimum read length that will be extracted from the greengenes database. Should be ~50-100 bases below the expected length of the PCR product.
max_read_length –> The maximum read length that will be extracted from the greengenes database. Should be ~50-100 bases above the expected length of the PCR product.