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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
364 stars 97 forks source link

Output directory #687

Closed susheelbhanu closed 1 year ago

susheelbhanu commented 1 year ago

Hey @SilasK,

Thanks for a great and well-designed tool. I was looking for it, but couldn't find it easily, but is there a way to specify an output directory when running the following?

atlas run assembly. Something along the lines of atlas run assembly -o <path/to/out_dir>

Also, similarly, is there an option to provide the samples.tsv for the same command above? The use case here being that, I will generate the samples.tsv file by myself.

My current workaround looks something like this: atlas run assembly -w $(dirname {input.tsv}) -c {input.conf}, where the input.tsv is my sample.tsv file

Thank you, Susheel

SilasK commented 1 year ago

I found it a good idea to keep the samples.tsv in the working directory.

You can create it yourself, no problem. I suggest you to copy or symlink your input.tsv to the output / working directory.

I have projects for modularizing atlas. Starting eith the assembly. With them there would be more options to specify an output directory..

susheelbhanu commented 1 year ago

Ok great, thank you!

This works for me for the moment, so all is good. Thanks again for a one-stop-shop!