added script comments

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