rnaseq-nf pipeline

A basic pipeline for quantification of genomic features from short-read data, implemented with Nextflow.

Requirements

• Unix-like operating system (Linux, macOS, etc)
• Java 17

Quickstart

1. Install Docker if you don't have it already.

2. Install Nextflow (version 25.10 or later):

   curl -s https://get.nextflow.io | bash
   

3. Launch the pipeline:

   ./nextflow run nextflow-io/rnaseq-nf -profile docker
   

4. When the run completes, open the following report in your browser:

   results/multiqc_report.html
   

You can view an example report in the MultiQC documentation.

Workflow diagram

Here is the workflow diagram of rnaseq-nf, generated by Nextflow using -with-dag:

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#B6ECE2',
      'primaryTextColor': '#160F26',
      'primaryBorderColor': '#065647',
      'lineColor': '#545555',
      'clusterBkg': '#BABCBD22',
      'clusterBorder': '#DDDEDE',
      'fontFamily': 'arial'
    }
  }
}%%
flowchart TB
    subgraph " "
    v0["channel.fromFilePairs"]
    v1["transcriptome"]
    v7["config"]
    end
    subgraph "RNASEQ [RNASEQ]"
    v2(["INDEX"])
    v3(["FASTQC"])
    v4(["QUANT"])
    end
    v8(["MULTIQC"])
    subgraph " "
    v9[" "]
    end
    v5(( ))
    v0 --> v3
    v0 --> v4
    v1 --> v2
    v2 --> v4
    v3 --> v5
    v4 --> v5
    v7 --> v8
    v5 --> v8
    v8 --> v9

Executors

The rnaseq-nf pipeline uses Nextflow to define the workflow logic separately from the underlying execution environment. This allows the pipeline to be executed seamlessly on a local machine, an HPC cluster, or a cloud provider, by simply applying a specific configuration profile.

Config profiles are provided for the following executors:

• AWS Batch (batch)
• Azure Batch (azure-batch)
• Google Batch (google-batch)
• SLURM (slurm)

By default, the pipeline executes tasks locally. Use the -profile option to run with a different executor:

nextflow run rnaseq-nf -profile slurm

You can also provide custom configuration for your environment, if none of the built-in profiles meet your needs. Create a nextflow.config file in the launch directory:

process {
    executor = 'uge'
    queue = 'my-queue'
}

The above example will make Nextflow submit jobs to a UGE cluster using the my-queue queue.

See the Nextflow documentation to learn more about Executors and Configuration.

Software dependencies

The rnaseq-nf pipeline uses the following software tools:

• Salmon
• FastQC
• MultiQC