search

ngless-toolkit / ngless

NGLess: NGS with less work
https://ngless.embl.de
Other
142 stars 24 forks source link

ofile= doesn't use output_directory #17

Closed unode closed 7 years ago

unode commented 7 years ago

Currently output generated by collect() is saved to the current directory instead of the directory specified via -o output_directory.

ngless -o output script.ngl

where script contains:

collect(count(mapped, features=['seqname']),
    current=sample,
    allneeded=readlines('input.txt'),
    ofile='output.tsv'

produces 'output.tsv' instead of 'output/output.tsv'.

luispedro commented 7 years ago

Let me think more about this.

The--output-directory argument where to write the semi-maintained HTML output as well as some automatically collected statistics. At the very least, this option is badly named. --html-report-output may be a better description?

In any case, resolving how to do meaningful stats output &c in the presence of collect() and friends is something to figure out before version 1.0.

unode commented 7 years ago

I see now that in previous uses I actually prepended "outputs/" to my output locations. So this is broader, not just affecting collect() but ofile= in general. If this is a target.

PS: This also explains why I was always getting an html report when I thought I was setting an output directory.