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cd
mkdir smrnaseq_cl
cd smrnaseq_cl
export NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1

• Line 1: Move to your home directory.

• 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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mkdir ~/rnaseq_pbs
cd ~/rnaseq_pbs

Create the script file smrnaseqrnaseq_test.sh by running the following command:

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

You can the script you just created using the command:

cat rnaseq_test.sh

Make the command executable and then submit your job to the PBS queue by running the following commands:

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