experiment.config

/*
** parameter name                   descriptions
** --------------                   ------------
** params.run_dir                   directory path to Illumina run directory (required)
** params.output_dir                directory path to processing pipeline output directory (required)
** params.sample_sheet              directory path to JSON samplesheet file (required)
** params.genomes_json              directory path to JSON genome file that has paths to required genome-related files (required)
**
** params.bcl2fastq_cpus            number of threads used by bcl2fastq (optional, default is 6)
** params.max_mem_bcl2fastq         maximum amount of memory used by bcl2fastq (optional, default is 40 GB total)
** params.demux_buffer_blocks       number of 8K byte blocks to use for demux output buffer (optional, default is 8192)
** params.index_recipe              index recipe for demultiplexing (optional, default is 0. Do not change this unless you know how.)
**
** params.trimmomatic_cpus          number of threads used by trimmomatic (optional, default is 4)
** params.trimmomatic_memory        maximum amount of memory used by trimmomatic (optional, default is 1 GB per cpu)
** params.bowtie_cpus               number of threads used by bowtie2 (optional, default is 6)
** params.bowtie_seed               bowtie aligner random number generator seed (optional)
** params.calculate_banding_scores  flag to enable banding score calculations (optional: true or false)
** params.make_genome_browser_files flag to enable making genome browser files (option: true or false)
** params.doublet_predict           flag to enable doublet prediction (optional: true or false)
** params.filter_blacklist_regions  flag to enable filtering blacklist regions when preprocessing cell_data_set (optional: true or false)
**
** process.maxForks                 maximum number of simultaneous process instances (optional, default is 20 as set in nextflow.config)
*/

params.run_dir = "path-to-Illumina-run-directory"
params.output_dir = "path-to-processing-pipeline-output-directory"
params.sample_sheet = "path-to-processing-pipeline-json-samplesheet-file"
params.genomes_json = "path-to-bbi-sciatac-analyze/genomes_stage.json"
params.calculate_banding_scores = false
params.make_genome_browser_files = false