Update file panaroo.sh

exercises/Pangenome_analysis/panaroo.sh

+
+
 #!/usr/bin/env bash
 #SBATCH --time=02:00:00
-#SBATCH --mem-per-cpu=20G
-#SBATCH --cpus-per-task=2
+#SBATCH --mem-per-cpu=64G
+#SBATCH --cpus-per-task=4
 #SBATCH --job-name=panaroo
-#SBATCH --output=panaroo_%j.out
-#SBATCH --error=panaroo_%j.err
+#SBATCH --output=slurm_panaroo_%j.out
+#SBATCH --error=slurm_panaroo_%j.err
 
 # Load singularity module
 module load singularityce
@@ -12,7 +14,7 @@ module load singularityce
 # Declare variables
 # input data folder 
 datadir=
-# results folder
+# results folder (03_output_mrsa)
 wd=
 # Path to singularity images folder
 singpath=/shares/amr.imm.uzh/bioinfo/singularity/
@@ -25,15 +27,17 @@ cd $wd
 mkdir -p panaroo/annotation_files
 mkdir -p panaroo/panaroo_output
 
+
 # generate soft links to the .gff files while looping through the sample names
 for sample_id in "${array[@]}"
 do
-	echo $sample_id
 	ln -s $wd/$sample_id/prokka_annotation/$sample_id.gff $wd/panaroo/annotation_files/
 done 
 
 # Runs singularity on the annotations and send the output to the output folder
 echo Starting panaroo $(date +"%T")
-cd panaroo
-$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes --core_threshold
+cd $wd/panaroo
+$singpath/panaroo_1.3.0--pyhdfd78af_0.sif \
+panaroo -i ./annotation_files/*.gff -o ./panaroo_output/ \
+--clean-mode strict --remove-invalid-genes --core_threshold 0.95 -t $SLURM_CPUS_PER_TASK
 echo Done $(date +"%T")
\ No newline at end of file