#!/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
#