Hi all, I’m wondering how input samples are used in the nf-core ChIP-seq workflow. If I have three replicates of both input and IP samples, and I create a sample sheet with replicate labels like '_Rep1', how does the workflow handle the input samples? Does it use the corresponding input replicate for each IP replicate (e.g., Input_Rep1 for Sample_Rep1), or does it merge all input replicates into one and use that for every IP replicate? Also, is it possible to customize the sample sheet like this:

Sample_Rep1,,,Input_Rep1
Sample_Rep2,,,Input_Rep2
Input_Rep1,,,
Input_Rep2,,,

Or like this:

Sample_Rep1,,,Input
Sample_Rep2,,,Input
Input_Rep1,,,
Input_Rep2,,,

I know the first option might seem unusual, but I’m new to ChIP-seq and unsure which approach is best practice. Thank you for your help!