typo fix on cpu options and ignore rerun on cached file

Author: hyphaltip

pipeline/01_domains_CAZY.sh

@@ -54,21 +54,22 @@ INFILE=$(ls $PROTEINS/*.${EXT} | sed -n ${IN}p)
 OUT=$DOMAINS/CAZY/$(basename ${INFILE} .${EXT})
 echo "processing $INFILE"
 rsync -a $CAZY_FOLDER $SCRATCH
-if [ ! -f ${OUT}.tsv ]; then
-    module load hmmer/3.3.2-mpi
+if [ ! -s ${OUT}.tsv ]; then
+    module load hmmer/3.3.2
     # hmmscan --cpu $CPUS --domtbl ${OUT}.domtbl -o ${OUT}.hmmscan $CAZY_DB $INFILE
     #srun hmmscan --mpi --domtbl ${OUT}.domtbl -o ${OUT}.hmmscan $SCRATCH/$(basename $CAZY_FOLDER)/$(basename $CAZY_DB) $INFILE
-    hmmscan --cpus $CPUS --domtbl ${OUT}.domtbl -o ${OUT}.hmmscan $SCRATCH/$(basename $CAZY_FOLDER)/$(basename $CAZY_DB) $INFILE
+    hmmscan --cpu $CPUS --domtbl ${OUT}.domtbl -o ${OUT}.hmmscan $SCRATCH/$(basename $CAZY_FOLDER)/$(basename $CAZY_DB) $INFILE
     bash $CAZY_FOLDER/hmmscan-parser.sh ${OUT}.domtbl | sort > ${OUT}.tsv
     module unload hmmer
 fi
 
 if [[ ! -d $OUT.run_dbcan || ! -f $OUT.run_dbcan/overview.txt ]]; then
     module load run_dbcan    
-    module load hmmer/3
-    #rsync -a /srv/projects/db/CAZY/CAZyDB/v11.0/dbCAN_sub.hmm 
+    module load hmmer/3.3.2
     export CAZY_FOLDER=$SCRATCH/$(basename $CAZY_FOLDER)
-    run_dbcan --db_dir $CAZY_FOLDER --out_dir $OUT.run_dbcan --tools all \
+    if [ ! -s $OUT.run_dbcan/overview.txt ]; then
+    	run_dbcan --db_dir $CAZY_FOLDER --out_dir $OUT.run_dbcan --tools all \
 	    --dbcan_thread $CPUS --hmm_cpu $CPUS --dia_cpu $CPUS \
 	    --use_signalP=TRUE --signalP_path $(which signalp) $INFILE protein 
+    fi
 fi