duplicates are always removed

[sunta3iouxos]

Description of the bug

Hi there I also asked this on the slack channel, but here is also:
Question regarding mapping and duplicates removal.
in my nf-param file there are these settings

"skip_removeduplicates": true,
"minimum_alignment_q_score": 2,

But, samtools view tells a different story:

samtools view -@32 -c -F260  NGS_A006200317_K36me3_K16ac_CUTandRUN/02_alignment/bowtie2/target/AA5_H3K36me3_R1.target.filtered.bam
18764748
samtools view -@32 -c NGS_A006200317_K36me3_K16ac_CUTandRUN/02_alignment/bowtie2/target/AA5_H3K36me3_R1.target.filtered.bam
18764748

It is as if there are no duplicate, from whatever source, no multiple alignments etc.
These bam files are clean, as far as I can see and I do not think that this is optimal for the CUTandRUN or CUT and Tag mapping and further analysis (edited)

Command used and terminal output

nextflow run nf-core/cutandrun -r 3.2.2 -profile singularity -c nextflow.config -work-dir /scratch/tmp/ -resume -params-file /scratch/NGS_A006200317_K36me3_K16ac/nf-params_new.json

Relevant files

No response

System information

Nextflow version (24.10.0)
Hardware (HPC )
Executor (slurm)
Container engine: (Singularity)
OS (CentOS Linux)
Version of nf-core/cutandrun (3.2.2)