# prepare input files for orthofinder
mkdir input_pep
cp ../11.reference_v2/pep/primary_transcripts/*.pep.fa input_pep
mkdir input_pep/core
mkdir input_pep/outgroup
mv input_pep/EA.pep.fa input_pep/outgroup
mv input_pep/EM.pep.fa input_pep/outgroup
mv input_pep/ZJ.pep.fa input_pep/outgroup
mv input_pep/*.pep.fa input_pep/core
for i in input_pep/*/*.pep.fa; do
    base=$(basename "$i" .pep.fa)
    echo "Processing $base"
    sed -i "s/>/>${base}@/g" "$i"
done

# run orthofinder with Hippophae genomes as backbone
pueue add -- orthofinder -t 12 -a 4 -f input_pep/core -o orthofinder_out

# assign outgroups
pueue add -- orthofinder -t 12 -a 4 --assign input_pep/outgroup --core orthofinder_out/Results_Hippophae_only