Problem with MACS2

[KarenLRdePaiva]

The current Socrates workflow requires MACS2, which is outdated and no longer available on Bioconda. Instead, the Bioconda repository provides MACS3 (the successor to MACS2) and MACSr . This discrepancy requires manual intervention to replace the use of MACS2 in the system with MACS3 or MACSr, which is not optimal for automation and reproducibility.

Proposed Solution:
Update the SOCRATES workflow to support MACS3 or MACSr, ensuring compatibility with the new software versions.
Modify the dependencies in the system requirements to specify MACS3 or MACSr instead of MACS2.
Perform testing to confirm that replacing MACS2 with MACS3 or MACSr maintains or improves the workflow's functionality and outputs.