dib-lab
'basename' may not be properly quoted
a student used a space in 'basename' in the config yaml file, and it looks like that will break shell commands that aren't properly quoted. I think single quotes should work.
we can add in some tests that do this for basenames containing $ and :)
Even if properly quoted, wouldn't this break all commands with assemblies (assembly names become {basename}_ext.fasta)?
On Wed, Jan 30, 2019 at 08:14:12AM -0800, Tessa Pierce wrote:
Even if properly quoted, wouldn't this break all commands with assemblies (assembly names become
{basename}_ext.fasta)?
I don't think so - any valid UNIX filename should work, no?
although I can imagine many actual programs barfing :)
an alternative is to put in requirements for basename (only alphanumeric, _, -, and .?)
best, --titus
C. Titus Brown, [email protected]