emel_lb1234.input

#input file for prepping the 4 plates of trees from linda

#input fastq files
file1=/home/gdu/projects/borevitz/reads/raw/Project_SN7001117R_0098_RSB_NAitken_GBS/Sample_Emeliodora_Blk1_4/Emeliodora_Blk1_4_NoIndex_L008_R1_001.fastq.gz
file2=/home/gdu/projects/borevitz/reads/raw/Project_SN7001117R_0098_RSB_NAitken_GBS/Sample_Emeliodora_Blk1_4/Emeliodora_Blk1_4_NoIndex_L008_R2_001.fastq.gz

#fastqc params
fastqc_outdir=/borevitz/megan/emelliodora/qc/emel_lb1234

#sequencing and sample information
lane_name=Emel_lb1234
barcode_file=Emelliodora_LB_Blocks1234_barcodes.tab

#user group for output
user=Eucalyptus

#number of threads to use
threads=11

#path to data
gbs_path="/borevitz/gbs/samples/"

#trim length for denovo
trimlen=88