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The nf-core/rnaseq workflow requires Nextflow to be installed on your HPC account. Find details on how to install and test Nextflow here. Prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.
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| Code Block |
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#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/smrnaseq -r 2.1.0 \
-profile singularity \
--outdir outdir \
--input samplesheet_saliva.csv \
--genome GRCh38 \
--three_prime_adapter 'AACTGTAGGCACCATCAAT'\
--fastp_min_length 18 \
--fastp_max_length 30 |
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