count_peaks bug

[igordot]

There is a problem with the count_peaks step that you added. At the beginning, you are reading the input variables:
source ./code/code.main/scripts-read-job-vars $branch "$objects" "genome genome_dir"

But then you are just scanning the directory manually, so you are ignoring them.

Simple example where this makes a difference:
All the peak counts are currently reported, including inputs, which doesn’t really make sense. Inputs should be ignored. It looks like you used the chipseq-diffbind step as an example (there is still chipseq-diffbind code in there). If you check the chipseq-diffbind step, it ignores the inputs.

I think the relevant part is the foreach obj ($objects) loop.