config.yml

### Path to software
piscem_path: "/fs/cbcb-lab/rob/students/noor/Atacseq/piscem_combine"

### afa path
afa_path: "/fs/cbcb-lab/rob/students/noor/Atacseq/alevin-fry/target/release/alevin_fry_atac"

### Reference
ref_genome: "/fs/nexus-projects/scATAC-seq/reference/GRCh38-2020-A-build/Homo_sapiens.GRCh38.dna.primary_assembly.fa"

### Piscem parameters
k: 25
m: 17
tmp_dir: "/scratch0"
threads: 16
threshold: 0.7
bin_size: 1000
permit_list_path: "/fs/cbcb-lab/rob/students/noor/Atacseq/cellranger-atac-2.1.0/lib/python/atac/barcodes/737K-cratac-v1.txt"
rev_comp: true

### fastq files
read1: "/fs/nexus-projects/scATAC-seq/data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fastqs/10k_pbmc_ATACv2_nextgem_Chromium_Controller_S3_L001_R1_001.fastq.gz"
read2: "/fs/nexus-projects/scATAC-seq/data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fastqs/10k_pbmc_ATACv2_nextgem_Chromium_Controller_S3_L001_R3_001.fastq.gz"
barcode: "/fs/nexus-projects/scATAC-seq/data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fastqs/10k_pbmc_ATACv2_nextgem_Chromium_Controller_S3_L001_R2_001.fastq.gz"

### output
out_path: "/fs/cbcb-scratch/npsingh/alevin_fry_atac_output"