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…2322)
This PR fixes#2321 so that more than one output line is placed in the
CSV. Oops!
It also adds a notification of what the CSV output file name is.
Last but not least, it supports `--output-dir` as a way to set the base
path for all output files.
Fixes#2321.
TODO:
- [x] add tests
- [x] make sure filename output behavior is documented
- [x] consider adding an option to have multigather save CSV results in
some other way, like by md5 or ...something. - punted to
#2328
when running:
the resulting file
SRR606249.trim.fq.gz.csv
(which is based on the query signaturefilename
property... ugh) only contains the first result.this code is at fault in
commands.py::multigather
:where the last line should be deindented so that it is run every time through the loop.
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