Commit 300e8e7f authored by eortega's avatar eortega
Browse files

Merge branch 'Check_run_post_restructure' into 'master'

Check run post restructure

See merge request !5
parents fe922c14 e54f91ae
#!/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)
......
......@@ -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}
......
......@@ -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
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