2026-08-02

99.scripts_v2/02.orthofinder.sh

@@ -0,0 +1,21 @@
+# 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
+