Error when passing directories for training

[plantformatics]

Hello,

First off, I want to say thank you for producing this tool. A little bit on the experimental design: I have ATAC-seq data from hundreds of donors, some with very high coverage, some with minimal sequencing depth. I want to train a model on the thoroughly sequenced donors (~25) to de-noise the remaining samples. The heavily sequenced donors are quite diverse and reflect the genetic diversity present in the cohort.

My issue arises when passing AtacWorks train the input data. Specifically, I am getting the following error:

atacworks train: error: argument --cleanpeakfile: expected one argument

I am passing --noisybw, --cleanbw, and --cleanpeakfile directory paths containing the noisy bigwigs, clean bigwigs, and clean narrowPeak files, respectively. I haven't tried using a comma separated list yet. Given the tutorial appendix 3 states that one can pass directories as input arguments, I thought I would I bring this to light so adjustments can either be made to the tutorial or to the code to make specifying input this way possible.

Thanks again for constructing this tool,

Alex

[plantformatics]

Update: Turns out there was a mismatch in variable names (peak vs. peaks) and the peaks folder wasn't being passed to atackworks. Training is running without issue. Sorry for the confusion!