Add README

parent b27830b3
...@@ -5,5 +5,7 @@ ...@@ -5,5 +5,7 @@
*.json *.json
*.sh.o* *.sh.o*
*.sh.po* *.sh.po*
*dijen*.o*
*dijen*.po*
*.failed *.failed
#*# #*#
\ No newline at end of file
# STR detection pipeline
ASDP PIPELINE
Author: anne-sophie.denomme-pichon@u-bourgogne.fr
Version: 0.0.1
Licence: FIXME
Description: How to launch scripts to get STR genotype from genomes on all the locus tested
1. Create genomes.list
2. Specify output file in launch_pipeline.sh
Warning, don't overwrite existing files
3. Launch launch_pipeline.sh
```bash
nohup ./launch_pipeline.sh &
```
Dependencies :
- genomes.list
- pipeline.sh
- launch_ehdn.sh
- launch_expansionhunter.sh
- launch_gangstr.sh
- launch_transfer.sh
- launch_tredparse.sh
- wrapper_delete.sh
- wrapper_ehdn.sh
- wrapper_expansionhunter.sh
- wrapper_gangstre.sh
- wrapper_transfer.sh
- wrapper_tredparse.sh
4. Launch getResults.py
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...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
## ehdn_getmanifest.sh ## ehdn_getmanifest.sh
## Version : 0.0.1 ## Version : 0.0.1
## Licence : FIXME ## Licence : FIXME
## Description : script to generate automatically a manifest by patient in a tsv format ## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
## Usage : ## Usage :
## Output : FIXME ## Output : FIXME
## Requirements : FIXME ## Requirements : FIXME
...@@ -14,11 +14,13 @@ ...@@ -14,11 +14,13 @@
## last revision date : 20200215 ## last revision date : 20200215
## Known bugs : None ## Known bugs : None
EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
REFERENCE="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
WORKDIR="/work/gad/shared/analyse/STR/pipeline" WORKDIR="/work/gad/shared/analyse/STR/pipeline"
cd "$WORKDIR" cd "$WORKDIR"
# Generate manifest by patient for all patients (to write file) # Generate manifest and multisampleprofile by patient for all patients (to write file)
for case in dijen* for case in dijen*
do do
# Generate manifest for one patient with all samples (to write lines in the file) # Generate manifest for one patient with all samples (to write lines in the file)
...@@ -31,6 +33,11 @@ do ...@@ -31,6 +33,11 @@ do
echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json" echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
fi fi
done > "$WORKDIR/$case/ehdn/$case.manifest.tsv" done > "$WORKDIR/$case/ehdn/$case.manifest.tsv"
# Generate multisampleprofile for one patient with all samples
"$EHDN" merge \
--reference "$REFERENCE" \
--manifest "$WORKDIR/$case/ehdn/$case.manifest.tsv" \
--output-prefix "$case/ehdn/$case"
done done
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