Add Vercel configuration for rewrites and build settings

99.scripts/workflow/transcripts_assembly/01.denove_assembly.sh

@@ -0,0 +1,31 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+MAX_MEMORY=${MAX_MEMORY:-"20G"}
+VIRIDI=${VIRIDI:-"$PROJECTHOME/01.reference/viridiplantae_odb12/"}
+ROSALES=${ROSALES:-"$PROJECTHOME/01.reference/rosales_odb12/"}
+
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <reads_1.fastq> <reads_2.fastq> <stem> <threads>"
+    echo "Perform de novo transcriptome assembly using Trinity"
+    exit 1
+fi
+
+fq1=$1
+fq2=$2
+stem=$3
+outdir="$stem"_trinity_out_dir
+THREADS=$4
+
+
+# Run Trinity for de novo transcriptome assembly
+Trinity --seqType fq --left "$fq1" --right "$fq2" --CPU "$THREADS" --max_memory "$MAX_MEMORY" --output "$outdir"
+# Get Longest isoform per gene
+perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$outdir.Trinity.fasta" >"$outdir".longest_isoform.fasta
+# BUSCO assessment
+busco -i "$outdir".longest_isoform.fasta -l "$VIRIDI" -m tran --cpu "$THREADS" -o "$outdir"_busco_viridi -f
+busco -i "$outdir".longest_isoform.fasta -l "$ROSALES" -m tran --cpu "$THREADS" -o "$outdir"_busco_rosales -f
+# Length Statistics
+TrinityStats.pl "$outdir.Trinity.fasta" >"$outdir".Trinity.fasta.length_stat.txt
+# Clear temporary directory
+rm -rf "$outdir"