evaluate using chipseq qc template for cutandrun output

[abartlett004]

Input for chipseq qc and whether it is available in cutandrun output:

1. coldata_fn: yes, use nfcore samplesheet

2. multiqc_data_dir:

• multiqc_fastqc.txt: yes, needed for total reads
• multiqc_samtools_stats.txt: yes, needed for mapped reads, mapped reads pct
• multiqc_phantompeakqualtools.txt: no. needed for nsc, rsc, but cutandrun doesnt run this tool. maybe can calculate another way?
• multiqc_frip_score-plot.txt: no. needed for frip, but maybe can calculate another way? confusing that this is absent because nf-core output documentation suggests there should be a FRiP score section in their multiqc report. maybe absent because of processes that we skipped?
• multiqc_peak_count-plot.txt: yes, but named multiqc_primary_peakcounts_plot.txt
• mqc_picard_deduplication_1.txt: yes, needed to calculate nrf

3. peaks_dir: yes

4. counts_fn: no. there are no deseq2 processes run in this pipeline, nor any other processes that would fragment the genome into bins and calculate counts