Quote arguments in shell scripts #348
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I accidentally committed other things to this branch, so I will have to redo the pull request. |
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When passing paths with unusual characters, e.g. spaces, quotes, braces or similar to flye, its calls to samtools and minimap2 fail.
That is because these calls go via a shell that interprets some characters in its own way. By adding single quotes around all paths when forwarding to the shell, the shell does not alter the paths but passes them correctly to the underlying program.
This pull request does exactly that.
It might be useful to squash the commits of this pull request when merging, as there are quite many with very small semantic contributions.