config.yaml

## Main parameters
# Pangenome name 
name: '<pangenome name>'
# Reference fasta (BGziped)
reference: '<reference_name>'
# Directory of apptainer images (downloaded with getApps.sh)
app.path: '<path>'

# Core parameters
# Wfmash alignement parameters :
wfmash.segment_length: 10000
wfmash.mapping_id: 95
wfmash.secondary: '-k 19 -H 0.001 -X'

# Seqwish parameters
seqwish.params: '-B 10000000 -k 19 -f 0'

# Odgi 1D and path coverage viz parameters 
odgi.1Dviz.params: '-x 2000 -b'
odgi.pcov.params: '-x 2000 -O'

## Optional parts of the workflow
# Running Quast to get statistics on input haplotypes
run_Quast: 'True'
# Getting figures showing chromosome decomposition into contigs
get_contig_pos: 'True'
# Computes Presence Absence Variant matrices for Panache (not recommended; very long)
get_PAV: 'False'
# Computes SyRI figures for haplotypes 
get_ASMs_SyRI: 'False' # Haplotype vs Reference
get_chrInputs_SyRI: 'False' # SyRI on chrInputs
# Creating final report
create_report: 'True'