Hello, I noticed that the

minimum_alignment_q_score

parameter is clearly defined (nextflow_schema.json)in the nf-core/cutandrun pipeline (default: 20), which helps filter low-quality alignments. However, I don’t see a similar threshold option in the nf-core/chipseq pipeline. Is MAPQ filtering handled differently there? @Jose Espinosa-Carrasco

hi, this parameter is not implemented in #CFP55NZ5G, could you open an issue in the repository?