config.yaml

---

pipeline: "ScNapBar"

# PATH TO INPUT DIRECTORY - all input files are relative to this directory
dir_in: "data"
# PATH TO OUTPUT DIRECTORY
dir_out: "results"
# TMP - temporary files
tmp_dir: /scratch/global_tmp/ 

# INPUT FILES - all files must be under dir_in
# Avoid dots in the file names before the extension(s)

# Annotations
# For the example use http://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz
reference_genome: "Homo_sapiens.GRCh38.dna.chromosome.17.fa" 
refFlat: "hg38.refFlat" # not used with option 1, otherwise make sure to uncompress the file!

# Cell Ranger - filtered_feature_bc_matrix
barcode: "barcodes.tsv.gz"
feature: "features.tsv.gz"
matrix:  "matrix.mtx.gz"
# Cell Ranger - raw_feature_bc_matrix/barcodes.tsv.gz
barcode_raw: "barcodes_raw.tsv.gz"
# Cell Ranger - outs
# ** Add the bam.bai index file to the same location
illumina_bam: "possorted_genome_bam.bam"

# Long reads 
nanopore_fq: "Nanopore.fq.gz"

# PARAMS
adapter: "CTACACGACGCTCTTCCGATCT"
polyTlength: 20
cdnalength: 32
umilength: 10
barcodelength: 16
numSimReads: 100000
numIlmReads: 1000000
cutoff: 50
percent_raw: 0.2
threads: 8
cdnaseq: "GCCTGGCTTGTTTGCAAAGGCCCTGGCCAACGTCAACATTGGGAGCCTCATCTGCAATGTAGGGGCCGGTGGACCTGCTCCAGCAGCTGG"

nano_seed: 1984 # Manually seeds the pseudo-random number generator (NanoSim)