config.yaml

# ASSEMBLY
## Path to directory containing metagenomic assemblies
assemblydir:
    #"assembly/spades/"

## Assembly Filename (Identical for each sample)
assemblyname:
  #"scaffolds.fasta"

# OUTPUT
## Path to directory to contain output results
outputdir:
    #"plastiC_results/"

# MAPPING 
## Do you require mapping? If true, please provide reads. If false, please provide alignment.bam.
maprequire:
    False

## Path to directory containing read files (Required if maprequire = True)    
readdir:
    #"reads/"

## Path to directory containing mapping bam files (Required if maprequire = False)
mapbamdir:
    #"reads2assembly/"

mapbamfile:
    #"alignment.bam"

# PLASTID BINS
##  Minimum % of bin to be plastid to retain as plastid bin
min_plastid_content:
    90


# DATABASES
## Paths to CAT database & taxonomy
catdbdir:
    #"databases/CAT_prepare_20210107/2021-01-07_CAT_database/"

cattaxdir:
    #"databases/CAT_prepare_20210107/2021-01-07_taxonomy/"

## Path to Uniref Diamond DB
unirefdb:
  #"databases/uniref100.KO.1.dmnd"