Fixes indenting and outdated messaging in run-escape-variants.sh help.
This is what the command line help looks like now:
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 - defaults to current directory
-w workdir directory that will hold a tempdir - 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Fixes indenting and outdated messaging in run-escape-variants.sh help. This is what the command line help looks like now:
Fixes #24