Workflow Type: Nextflow

nfcore/rnaseq

Build Status Nextflow Gitter

install with bioconda Docker Container available Singularity Container available

Introduction

nfcore/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.

The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) and performs extensive quality-control on the results (RSeQC, dupRadar, Preseq, edgeR, MultiQC). See the output documentation for more details of the results.

The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nfcore/rnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

These scripts were originally written for use at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).

Many thanks to other who have helped out along the way too, including (but not limited to): @Galithil, @pditommaso, @orzechoj, @apeltzer, @colindaven.

Version History

3.5 (latest) Created 18th Jan 2022 at 10:23 by Finn Bacall

Merge pull request #742 from nf-core/dev

Dev -> Master for v3.5 release


Frozen 3.5 646723c

2.0 Created 18th Jan 2022 at 10:22 by Finn Bacall

Merge pull request #488 from nf-core/dev

dev > master for 2.0 release


Frozen 2.0 bc5fc76

1.0 (earliest) Created 18th Jan 2022 at 10:22 by Finn Bacall

Merge pull request #61 from nf-core/dev

Dev > Master, v1.0 release


Frozen 1.0 44f1525
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Created: 18th Jan 2022 at 10:22

Last updated: 18th Jan 2022 at 10:23

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