#
# Samples: sample1, sample2, sample3, sample4, sample5
#
#
# Starting Workflow
#
#
# Global Variables:
# resample: 0
# wait: 1
# auto_input: 1
# coerce_paths: 1
# auto_name: 1
# indir: t/example/data/raw/test005
# outdir: t/example/data/processed/test005
# min: 1
# override_process: 0
# rule_based: 1
# verbose: 1
# create_outdir: 1
# file_rule: (.*).csv
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test005
# Outdir: $Bin/example/data/processed/test005/backup
#
cp $Bin/example/data/raw/test005/${SAMPLE}.csv $Bin/example/data/processed/test005/backup/${SAMPLE}.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test005/backup
# Outdir: $Bin/example/data/processed/test005/grep_VARA
#
echo "Working on $Bin/example/data/processed/test005/backup/${SAMPLE}.csv"
grep -i "VARA" $Bin/example/data/processed/test005/backup/${SAMPLE}.csv >> $Bin/example/data/processed/test005/grep_VARA/${SAMPLE}.grep_VARA.csv
wait
#
# Ending grep_VARA
#
#
#
# Starting grep_VARB
#
#
# Variables
# Indir: $Bin/example/data/processed/test005/grep_VARA
# Outdir: $Bin/example/data/processed/test005/grep_VARB
#
grep -i "VARB" $Bin/example/data/processed/test005/grep_VARA/${SAMPLE}.grep_VARA.csv >> $Bin/example/data/processed/test005/grep_VARB/${SAMPLE}.grep_VARA.grep_VARB.csv
wait
#
# Ending grep_VARB
#
#
# Ending Workflow
#