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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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'basename' may not be properly quoted #63

Open ctb opened 5 years ago

ctb commented 5 years ago

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 :)

bluegenes commented 5 years ago

Even if properly quoted, wouldn't this break all commands with assemblies (assembly names become {basename}_ext.fasta)?

ctb commented 5 years ago

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, ctbrown@ucdavis.edu