Adds command line arguments for the escape-variant pipeline

[johnbradley]

Adds argument parsing to run-escape-variant.sh and setup-escape-variants.sh. The escape-variant pipeline will now run in a temp directory to allow running multiple pipelines at once as well as rerunning a pipeline. Users can supply the genome, input file directory, output directory, working directory, log directory, email on completion, toggle a surveillance mode and a debug mode.

The log configuration was moved out of the sbatch scripts to allow specifying a log location. Hard coded genome filenames have been removed for issue #7 with the exception of fixing bed positions that will be addressed in issue #6.

---

Here is the help output printed when running ./run-escape-variants.sh without any arguments.

Runs a Slurm pipeline determining escape variants in fastq.gz files.

usage: ./run-escape-variants.sh -g genome -i inputdir [-o outdir] [-w workdir] [-l logdir] [-e email] [-s] [-d]
options:
-g genome    *.fasta genome to use - required
-i inputdir  directory containing *.fastq.gz files to process - required
-o outdir    directory to hold output files and logs - defaults to current directory
-w workdir   directory that will hold a tempdir and logs - defaults to current directory
-l logdir   directory that will hold sbatch logs - defaults to /logs within outdir
-e email     email address to notify on pipeline completion - defaults to empty(no email sent)
-s           runs surveillance mode - default is run experimental mode
-d           debug mode - skips deleting the tempdir

NOTE: The input genome must first be indexed by running ./setup-variants-pipeline.sh.
NOTE: The inputdir, outdir, logdir, and workdir must be directories shared across the slurm cluster.

Fixes #8 #9