broadinstitute / viral-pipelines

viral-ngs: complete pipelines
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task illumina_demux does not tolerate spaces in input filenames #460

Open dpark01 opened 1 year ago

dpark01 commented 1 year ago

As evidenced by some recent runs by Sabrina of demux_only and demux_deplete, the illumina_demux task does not currently tolerate spaces in the filename of the input samplesheet (and likely other input files).

Add more double-quoting to the WDLs.

Low urgency/priority.