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Commit bdbdd9c0 authored by Vanni Benvenga's avatar Vanni Benvenga
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added script comments

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...@@ -6,24 +6,32 @@ ...@@ -6,24 +6,32 @@
#SBATCH --output=panaroo_%j.out #SBATCH --output=panaroo_%j.out
#SBATCH --error=panaroo_%j.err #SBATCH --error=panaroo_%j.err
# Load singularity module
module load singularityce module load singularityce
# Declare variables
# input data folder
datadir= datadir=
# results folder
wd= wd=
# Path to singularity images folder
singpath=/shares/amr.imm.uzh/bioinfo/singularity/ singpath=/shares/amr.imm.uzh/bioinfo/singularity/
# Use the input data folder to generate an array containing the sample names
array=($(ls $datadir | cut -f 1 -d '_' | uniq)) array=($(ls $datadir | cut -f 1 -d '_' | uniq))
# Move to the results folder, create input and output folders
cd $wd cd $wd
mkdir -p panaroo/annotation_files mkdir -p panaroo/annotation_files
mkdir -p panaroo/panaroo_output mkdir -p panaroo/panaroo_output
# gff file soft links # generate soft links to the .gff files while looping through the sample names
for sample_id in "${array[@]}" for sample_id in "${array[@]}"
do do
ln -s $wd/$sample_id/prokka_annotation/$sample_id.gff $wd/panaroo/annotation_files/ ln -s $wd/$sample_id/prokka_annotation/$sample_id.gff $wd/panaroo/annotation_files/
done done
# Runs singularity on the annotations and send the output to the output folder
echo Starting panaroo $(date +"%T") echo Starting panaroo $(date +"%T")
cd panaroo 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 $singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes
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