adapt external script to posix style in case it's uploaded from windows

exec_scripts/localComparison.sh

@@ -6,6 +6,7 @@ unlock=$1
 if [[ $unlock == true ]]; then
 snakemake --profile config/profiles/localComparison --unlock &>> biseps.txt 
 fi
+tr -d '\15\32' < exec_scripts/script.sh > exec_scripts/script.sh 
 source exec_scripts/script.sh 
 snakemake --profile config/profiles/localComparison &>> biseps.txt 
 snakemake --profile config/profiles/localComparison  --report report.html &>> biseps.txt 

exec_scripts/localScript.sh

@@ -7,6 +7,7 @@ unlock=$1
 if [[ $unlock == true ]]; then
 snakemake --profile config/profiles/local --unlock &>> biseps.txt 
 fi
+tr -d '\15\32' < exec_scripts/script.sh > exec_scripts/script.sh 
 source exec_scripts/script.sh 
 snakemake --profile config/profiles/local &>> biseps.txt 
 snakemake --profile config/profiles/local --report report.html   &>> biseps.txt

exec_scripts/slurmComparison.sh

@@ -5,6 +5,7 @@
 #SBATCH --output=biseps.txt
 unlock=$1
 [ -e failed.comparison ] && rm -- failed.comparison
+tr -d '\15\32' < exec_scripts/script.sh > exec_scripts/script.sh 
 source exec_scripts/script.sh 
 if [[ $unlock == true ]]; then
 snakemake --profile config/profiles/slurmComparison --unlock

exec_scripts/slurmScript.sh

@@ -5,6 +5,7 @@
 #SBATCH --output=biseps.txt
 unlock=$1
 [ -e failed.alignment ] && rm -- failed.alignment
+tr -d '\15\32' < exec_scripts/script.sh > exec_scripts/script.sh 
 source exec_scripts/script.sh 
 if [[ $unlock == true]]; then
 snakemake --profile config/profiles/slurm --unlock