3) Preparing and running NGS_RNA pipeline

1) Copy rawdata to rawdata ngs folder

scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX username@yourcluster:${root}/groups/$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 username@yourcluster:/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_RNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_RNA/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

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