runParams.yml

##### Required Analysis Parameters
# Run "nextflow run path/to/ScaleTagToolkit --help" for a full list and documentation
# Also see "nextflow.config" for defaults

##### Inputs
### Sequencing data input can be either a Illumina sequencer RunFolder (bcl)
runFolder : s3://scale.pub/testData/uniATAC/PBMC/220222_NB552332_0226_AHH5KJBGXL/
### or a directory with fastq files
# fastqDir : "s3://scale.pub/testData/uniATAC/PBMC/220222_AHH5KJBGXL.fastq/"

### A file listing all samples in the analysis with their barcode sequences and sample settings
samples : ${projectDir}/docs/examples/samples.csv

#### Reference information
### Path to a .json file defining the reference genome
genome : ${projectDir}/docs/examples/genome.json

### BED file with peak coordinates to use for quantification (count matrix output)
### instead of per-sample de-novo calls
# peaks = "peaks.bed"