#
# A recipe demonstrating the use of parameters.
#

#
# Access parameters.
#
echo "Instrument: pacbio"
echo "Protocol: single"
echo "Cutoff: 0.05"
echo "Validate: True"
echo "Read length: 250"

#
# The files to be used.
#
echo "Reads: /export/sites/biostar-engine/export/media/projects/proj-tutorial/store-56bd2b99/genome.fa"
echo "SRR: /export/sites/biostar-engine/export/media/projects/proj-tutorial/store-e4c6e9e5/sra.txt"

#
# Make a nested directory structure
#
mkdir -p data/store/

#
# Create a few files.
#
cat /export/sites/biostar-engine/export/media/projects/proj-tutorial/store-56bd2b99/genome.fa | grep  ">"  > data/store/sequence-names.txt
cat /export/sites/biostar-engine/export/media/projects/proj-tutorial/store-e4c6e9e5/sra.txt > data/store/srr.txt

#
# Generate a table of contents.
#
find . -name '*' > contents.txt

#
# Print the contents to the screen
#
cat contents.txt
