Run - NGS

NGS_DNA

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Introduction

Release Notes

Environment setup with easybuild

Run

1) Copy rawdata to rawdata ngs folder
scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX [email protected]:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
2) Create a folder in the generatedscripts folder
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
3) Copy samplesheet to generatedscripts folder
scp –r TestRun.csv [email protected]:/groups/$groupname/${tmpDir}/generatedscripts/
Note: the name of the folder should be the same as samplesheet (.csv) file
4) Run the generate script
module load NGS_DNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_DNA/generate_template.sh .
sh generate_template.sh
cd scripts
Note: if you want to run locally, you should change in the CreateInhouseProjects.sh script the backend (this can be done almost at the end of the script where you have something like: sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh search for –b slurm and change it into –b localhost
sh submit.sh
5) Submit jobs
navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).
sh submit.sh

Dependencies

Workflow

Last modified 4yr ago

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Outline

1) Copy rawdata to rawdata ngs folder

2) Create a folder in the generatedscripts folder

3) Copy samplesheet to generatedscripts folder

4) Run the generate script

5) Submit jobs