From bdbdd9c0ca72c21cfc001b8c66413f9eff907a34 Mon Sep 17 00:00:00 2001
From: Vanni Benvenga <vanni.benvenga@gmail.com>
Date: Thu, 23 Mar 2023 13:30:06 +0100
Subject: [PATCH] added script comments
---
exercises/Pangenome_analysis/panaroo.sh | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/exercises/Pangenome_analysis/panaroo.sh b/exercises/Pangenome_analysis/panaroo.sh
index f3a700d..5de027a 100644
--- a/exercises/Pangenome_analysis/panaroo.sh
+++ b/exercises/Pangenome_analysis/panaroo.sh
@@ -6,24 +6,32 @@
#SBATCH --output=panaroo_%j.out
#SBATCH --error=panaroo_%j.err
+# Load singularity module
module load singularityce
+# Declare variables
+# input data folder
datadir=
+# results folder
wd=
+# Path to singularity images folder
singpath=/shares/amr.imm.uzh/bioinfo/singularity/
+# Use the input data folder to generate an array containing the sample names
array=($(ls $datadir | cut -f 1 -d '_' | uniq))
+# Move to the results folder, create input and output folders
cd $wd
mkdir -p panaroo/annotation_files
mkdir -p panaroo/panaroo_output
-# gff file soft links
+# generate soft links to the .gff files while looping through the sample names
for sample_id in "${array[@]}"
do
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
--
GitLab