Run - NGS

NGS_DNA

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Introduction

Release Notes

Environment setup with easybuild

Run

1) Copy rawdata to rawdata ngs folder
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scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX [email protected]:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
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2) Create a folder in the generatedscripts folder
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mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
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3) Copy samplesheet to generatedscripts folder
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scp –r TestRun.csv [email protected]:/groups/$groupname/${tmpDir}/generatedscripts/
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Note: the name of the folder should be the same as samplesheet (.csv) file
4) Run the generate script
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module load NGS_DNA
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cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
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cp $EBROOTNGS_DNA/generate_template.sh .
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sh generate_template.sh
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cd scripts
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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
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sh submit.sh
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5) Submit jobs
navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).
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sh submit.sh
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Dependencies

Workflow

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Contents

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