NGS_DNA
Search…
Run

1) Copy rawdata to rawdata ngs folder

1
scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX [email protected]:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
Copied!

2) Create a folder in the generatedscripts folder

1
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
Copied!

3) Copy samplesheet to generatedscripts folder

1
scp –r TestRun.csv [email protected]:/groups/$groupname/${tmpDir}/generatedscripts/
Copied!
Note: the name of the folder should be the same as samplesheet (.csv) file

4) Run the generate script

1
module load NGS_DNA
2
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
3
cp $EBROOTNGS_DNA/generate_template.sh .
4
sh generate_template.sh
5
cd scripts
Copied!
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
1
sh submit.sh
Copied!

5) Submit jobs

navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).
1
sh submit.sh
Copied!