How could I run the analysis with NFR only? My pipeline_info/paramsXXX.json has the right range of minFragmentLength(0) and maxFragmentLength (120). But the input bam file for macs3 callpeak is not limited to NFR. Are there any parameter(s) that I missed? Here is my command:
nextflow run dev_version/atacseq -profile singularity --input ./fastq.csv --min_trimmed_reads 0 --aligner bowtie2 --keep_dups TRUE --narrow_peak TRUE --genome hg38 --read_length 150 --outdir ./outDir_

Thanks,