Commit e6c1ab8a authored by peguerin's avatar peguerin
Browse files

04-renamed renamed into 04-ddocent

parent f2a6b988
......@@ -3,7 +3,7 @@
#argument 1 : path of the results 04-all_samples/species
mkdir -p 04-renamed/$1
mkdir -p 04-ddocent/$1
awk 'NR>1 { print $1"\t"$2"\t"$3"\t"$4}' $2 | while read LANE BARCODE POP SAMPLE ;
do
FILE_SE=`ls $(pwd)/03-samples/$LANE | grep "sample_"$BARCODE".fq.gz"`
......@@ -14,6 +14,6 @@ do
PATH_SE=$(pwd)/03-samples/$LANE/$FILE_SE
SAMPLE_EDIT=`echo $SAMPLE | sed 's/_/i/g'`
echo $PATH_SE
ln -s $PATH_SE "04-renamed/"$1"/"$POP"_"$SAMPLE_EDIT".F.fq.gz"
ln -s $PATH_SE "04-ddocent/"$1"/"$POP"_"$SAMPLE_EDIT".F.fq.gz"
fi
done
\ No newline at end of file
......@@ -161,7 +161,7 @@ Each fastq file belonging to a specific `{barcode}` is renamed by the correspond
bash 00-scripts/rename.sh {species} 01-infos/{species}_sample_information.csv
```
This command create a symlink of all fastq files such as `03-samples/{lane}/sample_{barcode}.fq.gz` is linked by `04-renamed/{species}/{pop}_{sample}.F.fq.gz`.
This command create a symlink of all fastq files such as `03-samples/{lane}/sample_{barcode}.fq.gz` is linked by `04-ddocent/{species}/{pop}_{sample}.F.fq.gz`.
## dDocent workflow
......@@ -179,8 +179,8 @@ FreeBayes is a Bayesian genetic variant detector designed to detect SNPs, INDels
**run dDocent workflow :**
* Go into the `04-renamed/{species}` folder.
* Then add a `04-renamed/{species}/reference.fasta` genome reference sequence file.
* Go into the `04-ddocent/{species}` folder.
* Then add a `04-ddocent/{species}/reference.fasta` genome reference sequence file.
* Now you can run the complete dDocent workflow. Type the following commands :
```
......
......@@ -24,13 +24,13 @@ CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
DDOCENT_CONFIG=/entrepot/working/seaconnect/seaConnect--dDocent/01-infos/ddocent_config.file
#### add a reference
ln -s /entrepot/donnees/genomes/"${SPECIES}"_genome.fasta 04-renamed/"${SPECIES}"/reference.fasta
ln -s /entrepot/donnees/genomes/"${SPECIES}"_genome.fasta 04-ddocent/"${SPECIES}"/reference.fasta
#### run the workflow "dDocent"
cd 04-renamed/"${SPECIES}"/
cd 04-ddocent/"${SPECIES}"/
singularity exec -B "/entrepot:/entrepot" $CONTAINER dDocent $DDOCENT_CONFIG
cd ../../
##filter remove indels
vcftools --vcf 04-renamed/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode-INFO-all --recode --out 05-vcf/"${SPECIES}"_snps &>10-logs/vcftools_"${SPECIES}".log
vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode-INFO-all --recode --out 05-vcf/"${SPECIES}"_snps &>10-logs/vcftools_"${SPECIES}".log
......
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