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cd $HOME/workshop/2024-2/session3
mkdir smrnaseq_cl
cd smrnaseq_cl
export NXF_OPTS='-Xms1g -Xmx4g'
nextflow pull file:///work/training/smrnaseq
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1

• Line 1: Move to the directory created for this workshop.

• Line 2: Make a temporary folder called smrnaseq_cl for Nextflow to test the smrnaseq pipeline.

• Line 3: Change directory to the newly created folder smrnaseq_cl.

• Line 4: In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this.

• Line 5: Download and run the test code.

This will download the smrnaseq pipeline and then run the test code. It should take ~20-30 minutes to run to completion.

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cat <<EOF > rnaseq_test.sh
#!/bin/bash -l
#PBS -N nfrnaseq_test
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=6:00:00

cd \$PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/rnaseq -r 3.14.0 -profile test,singularity --outdir results
EOF

• Line 3: Set your PBS job name to be nfrnaseq_test

• Line 4: Specify memory and CPU resource that you want to allocate to your job

• Line 5: Specify that you want to allocate 6h for your job to run to.completion

• Line 7: Change directory to $PBS_O_WORKDIR, which is a special environment variable created by PBS. This will be the folder where you ran the qsub command

• Line 8: Load java

• Line 9: In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this

• Line 10: Run the nf-core/rnaseq pipeline using the test data provided

You can check the content of the PBS script you just created using the command:

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