# path to sample sheet csv with columns for ID,forward,reverse,taxid,seed,gene
samples: config/samples.csv

# user email
user_email: user@example_email.com

# getorganelle reference (go_fetch, custom)
go_reference: go_fetch

# forward adapter
forward_adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

# reverse adapter
reverse_adapter: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

# fastp deduplication (True/False)
fastp_dedup: True

# barrnap kindgom (Bacteria:bac, Archaea:arc, Eukaryota:euk, None:NA)
barrnap_kingdom: euk

# alignment trimming method to use (gblocks or clipkit)
alignment_trim: gblocks

# alignment missing data threshold for alignment (0.0 - 1.0)
missing_threshold: 0.5

# name of outgroup sample (optional)
# use "NA" if there is no obvious outgroup
# if more than one outgroup use a comma separated list i.e. "sampleA,sampleB"
outgroup: Eurema_blanda

# plot dimensions (cm)
plot_height: 20
plot_width: 20
