How to remove some chromosomes, e.g., chrUn_KI270438v1

[liuyang2006]

Description of the bug

I use general pipeline, but I want keep only chr1-22, chrX, and chrY. Remove other chromosomes. My output file looks like below:

chr1    143263330       143263759       kmt2a_uocm1_wt_R3.macs2_peak_1  44      .       2.54556 10.5652 4.43496 114
chr17   26881280        26881514        kmt2a_uocm1_wt_R3.macs2_peak_2  320     .       2.97694 38.9967 32.0359 94
chr3    93470460        93470759        kmt2a_uocm1_wt_R3.macs2_peak_3  1984    .       1.76798 207.926 198.435 121
chr3    151098027       151098472       kmt2a_uocm1_wt_R3.macs2_peak_4  31      .       6.00315 9.18563 3.13759 286
chrM    3625    3971    kmt2a_uocm1_wt_R3.macs2_peak_5  94      .       1.3531  15.7527 9.43401 41
chrUn_KI270438v1        105660  105978  kmt2a_uocm1_wt_R3.macs2_peak_6  30      .       1.60841 9.12977 3.08933 276
chrUn_KI270467v1        2172    2393    kmt2a_uocm1_wt_R3.macs2_peak_7  563     .       1.74571 63.6946 56.3912 154
chrUn_KI270467v1        2919    3520    kmt2a_uocm1_wt_R3.macs2_peak_8  266     .       1.56439 33.4797 26.6181 507

Could you help to figure out how to remove chrUn_KI270438v1, these kind of chromosomes? Also, chrM. Thank you!

Best,
Yang

Command used and terminal output

nextflow run nf-core/cutandrun --input cut_n_run/00samplesheet_cut_n_run_batch2.csv -profile singularity --peakcaller seacr,macs2 --genome GRCh38

Relevant files

No response

System information

No response