SCCWRP_QIIME2_tax_param_062923_600_16S.sh

#!/bin/bash

#conda activate qiime2-2021.11 <----- MUST CONDA ACTIVATE BEORE RUNNING SCRIPT

homePATH="/home/genomics/raw" # Path to the parent directory.  Should NOT finish with "/"
workingPATH="/home/genomics/raw/biofilm_062923_500v600"  	#Path to  where the fastqs are stored. Should NOT finish with "/" It must be located in the parent directory.
fastq_directory="Apr_2023_V4V5_600_cycle_fastq"	# Name of the folder containing the fastqs. It must be located in the parent directory.
fastqPATH=$workingPATH/$fastq_directory
project_shortname="Apr_2023_V4V5_600_cycle"
refReads="062923_16S_V4V5_600_cycle_merger_3_rep_set" #DO NOT INCLUDE file type!

taxonomy="silva-138-99" #put only base name of taxonomy
taxonomy_names=$homePATH/$taxonomy"-tax.qza" #include file type!
taxonomy_fasta=$homePATH/$taxonomy"-seqs.qza" #include file type!

import_tax_yes_no="no" #only options are "yes" (taxonomy is in fasta/txt) or "no" (taxonomy is in qza)

#fill out below with specifics for primer set of interest
#only quotes around batch_size and orientation arguments
primerF=GTGYCAGCMGCCGCGGTAA
primerR=GGACTACNVGGGTWTCTAAT
id=0.95
length_min=200
length_max=450
jobs_num=20
batch_size="auto"
orientation="forward"
chunk=20000

############## source shell script with qiime commands ##############
. ./SCCWRP_QIIME2_tax_runfile.sh

############## source R script with dada2 commands ##############
# Rscript --vanilla /home/kyliel/mini_attempt/SCCWRP_comp_dada2.R $workingPATH $project_shortname $fastqPATH $primerF $primerR $lengthF $lengthR $truncQ $maxEE_F $maxEE_R
#arguments are put after R script file path and file name
#MUST MATCH ARGUMENTS FROM PARAMETERS FILE