Hi again, we are still thinking about getting a solution for both the ChIP as well as CUT&RUN workflow. We have just kicked off a test run of

bedtools genomecov

with

-bg

(the current method that produces bigWig files that have higher background at lower zoom levels), and

-bga

(the proposed change that produced more nuanced (and more aesthetic (=lower)) background levels). If it turns out that it produces nicer bigWig files but the resulting peak call files are largely unaffected thereof, we were thinking of putting in a PR with fix for that. It looks like the ChIP-seq workflow uses a local

genomecov

module and not the nf-core module for

bedtools genomecov

(see here: https://github.com/nf-core/chipseq/blob/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/local/bedtools_genomecov.nf#L30), so a single-letter substition from

-bg

to

-bga

might do the trick. Or should this rather be implemented in a more modular fashion using the nf-core module instead (that module uses

$args

as options, so one could probably pass it the 0-value option instead). Many thanks for any thoughts/comments!