Hostile crashes if path has spaces in it

[pvanheus]

Some Windows users have spaces in their usernames which propagate e.g. to the epi2melabs directory where hostile data is stored. This causes a crash in hostile.

[bede]

Thanks Peter – while FASTQ and index paths are quoted, e.g. BIN_PATH is not, which I imagine could cause this issue. Do you happen to know if the problem arises when accessing indexes, the minimap2/bowtie2 binaries, or something else?

[bede]

Is this still an issue @pvanheus? If not please could you give an example where it breaks? I've quoted BIN_PATH in 6ad8aebbdfc94ec173c8ae9a0e0978598dd50b84

[pvanheus]

Sorry, meant to close this. I verified that the problem wasn't with hostile itself.

[bede]

Thanks, just wanted to check!