Owl CITE-Seq-count Pipeline

This is an Owl Pipeline that runs CITE-Seq-Count in a CITE-seq and/or cell hashing experiment.

Pipeline Definition

An example pipeline definition file is:

# Version of the configuration file
version: 1

# Name of the pipeline
name: cite_seq_count

# Pipeline arguments
# Read1 fastq file location in fastq.gz format.
# Read 1 typically contains Cell barcode and UMI
read1: /storage/user/cite/5kPBMC/big_R1.fastq.gz
# Read2 fastq file location in fastq.gz.
# Read 2 typically contains the Antibody barcode.
read2: /storage/user/cite/5kPBMC/big_R2.fastq.gz
# The path to the csv file containing the antibody
# barcodes as well as their respective names.
tags: /storage/user/cite/5kPBMC/tags.csv
# First nucleotide of cell barcode in read 1
cell_barcode_first_base: 1
# Last nucleotide of the cell barcode in read 1
cell_barcode_last_base: 16
# First nucleotide of the UMI in read 1
umi_first_base: 17
# Last nucleotide of the UMI in read 1
umi_last_base: 28
# How many cells you expect in your run
expected_cells: 6000
# How many bases should we trim before starting to map
trim: 10
# Whitelist of cell barcodes provided as a csv file
whitelist: /storage/user/cite/5kPBMC/whitelist.csv
# Output
output: /storage/user/5kPBMC/output

# Extra arguments
# extra: ["--max-error", "3", "--no_umi_correction"]

# Resources requested
# Leave workers at 1
# Threads is the numbeer of cores
# Memory is the memory in Gi
resources:
  threads: 10
  workers: 1
  memory: 32