fold.settings

# Variables and auxiliary functions.

hairpin=ACGCCGGCGGCAAGTGAAGCCGCCGGCGT
hlen=`echo -n $hairpin | wc -c`

# Data directory containing fastq files, which must have .fastq.gz extension.
data=`pwd`/../data

# List of SAMPLE_LIB prefixes, for which there is at least one
# pair of R?.fasta.gz files in the $data directory.
# E.g. 'A666_HADES-1' for sample 'A666' with library 'HADES-1'
sample_lib_pairs="
A16132-AncPET50k_MCS45-05
"

# Extract unique sample names from $sample_lib_pairs.
samples=`for s in $sample_lib_pairs; do echo $s; done | cut -d_ -f1 | sort -u`

# List of references to use. Must have ".fasta" extension.
# The basename without ".fasta" will be used in filenames.
# E.g. 'foo_bar' is used for reference '/tmp/refs/foo_bar.fasta',
# and sample/lib A666_HADES-1 will have final bam 'A666.foo_bar.bam'.
refs="
/localscratch/Refs/Lambda/Lambda_BWA6_2_2016_11/Lambda.fasta
/localscratch/Refs/Bos_taurus/Bos_taurus_BWA6_2_2015_08/Cow_UMD3_1.fasta
"

# Number of threads to use for various tools.
nthreads=4
realigner_threads_per_sample=1 #$nthreads
bwa_threads_per_sample=$nthreads
sort_threads_per_sample=$nthreads # don't set this too high,
				  # as it runs concurrently with bwa


# Kills all subprocesses when parent process is killed (e.g. by CTRL-C).
#trap 'kill 0' EXIT

# Make exit status propagate through pipes.
set -o pipefail

# Print error message and exit.
die() {
	echo Error: $@
	exit 1
}

## load Environment Modules here, as required
#module load Python/2.7.13-foss-2016b
#module load BWA/0.7.15-foss-2016b
#module load SAMtools/1.4.1-foss-2016b
#module load Java/1.8.0_101 GATK/3.6-Java-1.8.0_101