config.yaml

# ----------------------------------------
# General

# path to sheet describing each cell
samplesheet: samplesheet.tsv

# the assembly pipeline uses the immcantation framework for IgBLAST
# gene segment calling and results parsing
# options: 'docker' or 'singularity'
container_type: docker

# Singularity only: if commands are required prior
# to singularity execution, uncomment and edit the line below
#singularity_pre_cmd: "module load system && module load singularity && "

# human or mouse
species: human

# partition (for cluster computing)
partition: "quake,owners"

# ----------------------------------------
# Assembly

receptor: BCR

# optional scratch environmental variable for cluster computing
#scratch: '$L_SCRATCH'

# ----------------------------------------
# Alignment

# sequencing read length e.g. 100 for 2x100 paired-end sequencing
# (used during STAR genome generation)
read_length: 100

# whether or not to include ERCCs in the genome fasta and gtf 
include_ERCCs: True

# STAR alignment: fasta and gtf files
# (these should not need to be changed)
fasta_url:
  human: ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
  mouse: ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

fasta_name:
  human: Homo_sapiens.GRCh38.dna.primary_assembly
  mouse: Mus_musculus.GRCm38.dna.primary_assembly

gtf_url: 
  human: ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz
  mouse: ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz

gtf_name:
  human: Homo_sapiens.GRCh38.93
  mouse: Mus_musculus.GRCm38.93