Nf-core-rnaseq

Introduction

nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.

Versions

• 3.14.0

Commands

• rnaseq

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=nf-core-rnaseq      # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load nf-core-rnaseq/XXXX        ### Latest version is recommended.