Add Vercel configuration for rewrites and build settings

99.scripts/workflow/transcripts_assembly/05.reduce_redundancy.sh

@@ -0,0 +1,27 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+IDENTITY=${IDENTITY:-0.99}
+THREADS=${THREADS:-6}S
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_dir> <output_dir> <extension>"
+    echo "Reduce redundancy of CDS files using cd-hit-est"
+    exit 1
+fi
+
+indir=$1
+outdir=$2
+ext=$3
+
+mkdir -p "$outdir"
+# Process each file in the input directory with the specified extension
+for cds in "$indir"/*."$ext"; do
+    stem=$(basename "$cds" ."$ext")
+    echo "Processing $cds($stem) ..."
+    echo "cd-hit-est -i $cds -o $outdir/$stem.cds_rr.fa -c $IDENTITY -n 10 -r 0 -T $THREADS"
+    cd-hit-est -i "$cds" -o "$outdir/$stem".cds_rr.fa -c "$IDENTITY" -n 10 -r 0 -T "$THREADS"
+    echo "seqkit translate $outdir/$stem.cds_rr.fa > $outdir/$stem.prot_rr.fa"
+    seqkit translate "$outdir/$stem".cds_rr.fa >"$outdir/$stem".prot_rr.fa
+    echo "Done."
+done