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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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output directory #39

Open mbourgey opened 5 years ago

mbourgey commented 5 years ago

Hi Jeremiah,

would it be possible to add an option to specify where the outputs should be written instead of using the current directory ? i don't think this maybe such a complicated task to do (maybe a bit time consuming I agree) but it would very help to make the software included in more broader pipeline.

Thank you

walaj commented 5 years ago

Thanks for your patience with this.

I just tried this out, and it turns out you can already do this. e.g.

svaba run -t <bam> -a /tmp/analysis_id

If you want the user to be able to just specify the output name in your pipeline, you could just concatenate in e.g. bash first.

alartin commented 5 years ago

Hi just get the same problem here, I wonder if the value of option -a is embedded somewhere in the output files? If this is case, I don't think is a good idea to expose such info and suggest an option of -o to explicitly define the output dir.

fgvieira commented 3 years ago

Any update on this issue?