assembler-opt does not play nicely with make again

[andersgs]

There is a bug in generating the Makefile when using nullarbor v1.30-dev with --assembler-opt for the again target. make again generates a nullarbor.pl command that has stripped the quotes around the assember options string.

For example, if I initially use this command line:

nullarbor.pl --name test --ref test.fa --input input.tab --outdir nullarbor --assembler shovill --assembler-opt "--gsize 5M"

When I use make again, I get the following command:

nullarbor.pl --name test --ref test.fa --input input.tab --outdir nullarbor --assembler shovill --assembler-opt --gsize 5M --force

Notice the options for assemble-opt are no longer quoted. I looked in to the code, but I couldn't really suss out where the issue is happening. I notice that when you use the variable $assembler-opt, you quote it. But, when generating the command for again taget, you modify the array @CMDLINE to strip any --force or -f that may exist. The modified @CMDLINE array is then printed. I wonder if there is a way to specifically quote an element of the array?

[tseemann]

Temporary hacks:

1. don't provide --gsize 5M as it will guess properly
2. use --gsize=5M instead