#!/bin/bash

#
# Generated at: 2015-12-10T09:35:49
# This file was generated with the following options
#	--workflow	config2.yml
#

#
# Samples: SAMPLE1, SAMPLE2
#
#
# Starting Workflow
#
#
# Global Variables:
#	ROOT: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
#	indir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
#	outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT
#	file_rule: (SAMPLE.*)$
#	by_sample_outdir: 1
#	find_by_dir: 1
#

#
#

# Starting copy1
#



#
# Variables 
# Indir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
# Outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/copy1
# Local Variables:
#	INPUT: {$self->indir}/{$sample}.csv
#	TRIMMOMATIC: {$self->ROOT}/{$sample}_TRIMMOMATIC_THING.gz
#	before_meta: 
#HPC mem=24GB
#	outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/copy1
#	indir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
#

echo "Working on /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE1/SAMPLE1.csv"
cp "/home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE1/SAMPLE1.csv" "/home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE1/copy1/SAMPLE1.csv"


echo "Working on /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2/SAMPLE2.csv"
cp "/home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2/SAMPLE2.csv" "/home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE2/copy1/SAMPLE2.csv"



wait

#
# Ending copy1
#


#
#

# Starting copy2
#



#
# Variables 
# Indir: {$self->ROOT}
# Outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/copy2
# Local Variables:
#	indir: {$self->ROOT}
#	INPUT: {$self->indir}/{$sample}.csv
#	before_meta: HPC THINGS

#
#HPC mem=24GB
#

#	outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/copy2
#

echo "Working on /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE1/SAMPLE1.csv" && \
    echo "This should be UNDEF /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2_TRIMMOMATIC_THING.gz" && \
    cp "/home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE1/SAMPLE1.csv" "/home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE1/copy2/SAMPLE1.csv"


echo "Working on /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2/SAMPLE2.csv" && \
    echo "This should be UNDEF /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2_TRIMMOMATIC_THING.gz" && \
    cp "/home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2/SAMPLE2.csv" "/home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE2/copy2/SAMPLE2.csv"



wait

#
# Ending copy2
#


#
# Starting FileDetails Plugin
#


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE1/copy1


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE1


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE2/copy1


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA/SAMPLE2


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE1/copy2


filedetails.pl --check_dir /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT/SAMPLE2/copy2


#
# Ending FileDetails Plugin
#
#
# Ending Workflow
#
