Merge branch 'Check_run_post_restructure' into 'master'

Check run post restructure

See merge request !5

phages/scripts/03_mapping.sh

 #!/bin/bash
 
+## Arguments in the order
+##      1- working directory
+##      2- name of the step
+##      3- name of the previous step
+##      4- link to fasta reference
+
+
 
 ## DEFINE PATH
 path=$1
 # path=/home/enrique/work/Gandon/coevolution/phages/
+step_name=$2
+prev_step=$3
+
+# ref=data/refs/Sv2972/
+ref=$4
+
 
 
 ## CREATE INDEXES AND 
@@ -14,13 +27,27 @@ path=$1
 # bowtie2 --phred33 -5 12 -p 35 -t -x ${path}data/refs/indexes_Sv/Sv -1 ${path}data/trimmed/W_seq/W4T3_S54_R1.fq.gz -2 ${path}data/trimmed/W_seq/W4T3_S54_R2.fq.gz -S ${path}results/test.sam
 
 
-path_fasta=${path}data/trimmed/
+## CHECK FOR INDEXES
+
+test -f  ${ref/.fasta}.1.bt2
+if [ $? -eq 1 ];
+    then
+        echo 'Index for bowtie2 not present near fasta file'
+        bowtie2-build  $ref  ${ref/.fasta}
+    echo 'Created index for bowtie2'
+fi
+
+
+
+
+
+path_fasta=${path}steps/${prev_step}
 
-path_results=${path}results/
+path_results=${path}steps/${step_name}/
 
-bacteria_index=${path}data/refs/indexes_St/St
+# bacteria_index=${path}data/refs/indexes_St/St
 
-virus_index=${path}data/refs/indexes_Sv/Sv
+virus_index=${ref/.fasta}
 
 
 for i in  $(find  $path_fasta  -name *_R1.fq.gz)

phages/scripts/04_snpcalling.sh

@@ -2,13 +2,15 @@
 
 ## SNPCALLING
 
-wd=$1   ## Working directory's path
-ref=$2  ## path to reference.fasta
-od=$3   ## Output directory
+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
 
 
 
-for i in $(find results/mapping/ -type f -name *.bam)
+for i in $(find ${path}steps/${bam}/ -type f -name *.bam)
 do
     od2=$(dirname $i);
     od2=${od2/mapping/snpcalling}

phages/scripts/procedure.sh

@@ -56,3 +56,23 @@ done
 ###################################
 ## Trimm and clean
 ./scripts/02_trimm_and_clean.sh  $PWD/  trimming
+
+
+###################################
+## Mapping on virus
+## Arguments in the order
+##      1- working directory
+##      2- name of the step
+##      3- name of the previous step
+##      4- link to fasta reference
+./scripts/03_mapping.sh  $PWD/  map_on_phage  trimming  data/refs/Sv2972/NC_007019.1.fasta
+
+
+###################################
+## SNPcalling
+## Arguments in the order
+##      1- working directory
+##      2- name of the step
+##      3- name of the previous step. The one which produced the bam files
+##      4- link to fasta reference
+./scripts/04_snpcalling.sh  $PWD/  snpcall_freebayes  mapping  data/refs/Sv2972/NC_007019.1.fasta