Wrangler app bad substitution error

[arisp99]

Bug Description

In #26, we implemented checks to ensure that arguments passed to the wrangler app had no spaces in them. Our solution relies on parameter expansion. Crucially, this is a non-POSIX feature. While our container does run using bash, this error would indicate that the parameter expansion is not working properly.

Reported by @iek.

[arisp99]

Not being able to perform parameter expansions causes errors in other places as well. The lines that need to be fixed are:

MIPTools/MIPTools.def

Lines 409 to 420 in d3e613c

	# Remove whitespace from arguments
	probe_sets=${probe_sets//[[:space:]]/}
	sample_sets=${sample_sets//[[:space:]]/}
	stitch_options=${stitch_options//[[:space:]]/}
	# Ensure that stitch options begin with a comma if not the default value
	# This is done as the arguments are fed in with leading dashes and the
	# python script will crash if dashes are fed in. By adding a leading comma,
	# the script will run.
	if [ ${stitch_options:0:1} != "," ] && [ ${stitch_options} != "none" ]; then
	stitch_options=",${stitch_options}"
	fi