corrected path management in scripts/04_snpcalling.sh typos correction

phages/scripts/01_quality_check.sh

@@ -32,7 +32,7 @@ echo $W_seq $R_seq $Other_seq
 
 
     ### CREATE SYMBOLIC LINKS TO SEQUENCE FILES
-    ### DIIVIDED IN 3 DIRECTORIES
+    ### DIVIDED IN 3 DIRECTORIES
 
 echo "CREATE SYMBOLIC LINKS"
 

phages/scripts/04_snpcalling.sh

@@ -2,21 +2,23 @@
 
 ## SNPCALLING
 
-path=$1   ## Working directory's path
+path=$1                     ## Working directory's path
 step_name=$2
-bam=$3  ## name of step which created the bam files to be used
-ref=$4  ## path to reference.fasta
-od=${path}${step_name}/   ## Output directory
+prev_step=$3                      ## name of step which created the bam files to be used
+ref=$4                      ## path to reference.fasta
 
+echo ${path}steps/
+mkdir -p ${path}steps/
 
 
-for i in $(find ${path}steps/${bam}/ -type f -name *.bam)
+for i in $(find ${path}steps/${prev_step}/ -type f -name *.bam)
 do
-    od2=$(dirname $i);
-    od2=${od2/mapping/snpcalling}
-    mkdir -p $od2
+    od=$(dirname $i)
+    od=${od/$prev_step/$step_name}
 
-    freebayes -b $i -f $ref -C 1 -K -F 0.01  > ${od2}/$(basename -s .sort.bam  $i).vcf
+    mkdir -p  $od
+
+    freebayes -b $i -f $ref -C 1 -K -F 0.01  > ${od}/$(basename -s .sort.bam  $i).vcf;
 
     echo $(basename -s .sort.bam  $i).vcf 'has been created';
 done