Nextflow pipeline template

scbirlab/nf-otemple is a Nextflow pipeline template.

Use it to scaffold a new pipeline project.

Table of contents

• Processing steps
• Requirements
• Quick start
• Inputs
• Outputs
• Issues, problems, suggestions
• Further help

Processing steps

Requirements

Software

You need to have Nextflow and either Anaconda, Singularity, or Docker installed on your system.

First time using Nextflow?

If you're at the Crick or your shared cluster has it already installed, try:

module load Nextflow Singularity

Otherwise, if it's your first time using Nextflow on your system and you have Conda installed, you can install it using conda:

conda install -c bioconda nextflow 

You may need to set the NXF_HOME environment variable. For example,

mkdir -p ~/.nextflow
export NXF_HOME=~/.nextflow

To make this a permanent change, you can do something like the following:

mkdir -p ~/.nextflow
echo "export NXF_HOME=~/.nextflow" >> ~/.bash_profile
source ~/.bash_profile

Quick start

Make a sample sheet (see below) and, optionally, a nextflow.config file in the directory where you want the pipeline to run. Then run Nextflow.

nextflow run scbirlab/nf-template

Each time you run the pipeline after the first time, Nextflow will use a locally-cached version which will not be automatically updated. If you want to ensure that you're using the very latest version of the pipeline, use the -latest flag.

nextflow run scbirlab/nf-template -latest

If you want to run a particular tagged version of the pipeline, such as v0.0.1, you can do so using

nextflow run scbirlab/nf-template -r v0.0.1

For help, use nextflow run scbirlab/nf-template --help.

The first time you run the pipeline for a project, the software dependencies in environment.yml will be installed. This may take several minutes.

Inputs

The following parameters are required:

• sample_sheet: path to a CSV with information about the samples and FASTQ files to be processed

The following parameters have default values which can be overridden if necessary.

• inputs = "inputs" : The folder containing your inputs.
• outputs = "outputs" : The folder to containing the pipeline outputs.

The parameters can be provided either in the nextflow.config file or on the nextflow run command.

Here is an example of the nextflow.config file:

params {
    sample_sheet = "/path/to/sample-sheet.csv"
    inputs = "/path/to/inputs"
}

Alternatively, you can provide the parameters on the command line:

nextflow run scbirlab/nf-template \
    --sample_sheet /path/to/sample-sheet.csv \
    --inputs /path/to/inputs

Sample sheet

The sample sheet is a CSV file providing information about which FASTQ files belong to which sample.

The file must have a header with the column names below, and one line per sample to be processed.

• sample_id: the unique name of the sample.

Here is an example of the sample sheet:

sample_id
sample01
sample02

Outputs

Outputs are saved in the directory specified by --outputs (outputs by default). They are organised these directories:

• multiqc: HTML reports from the outputs of intermediate steps

Issues, problems, suggestions

If you run into problems not covered here, add to the issue tracker.

Further help

Here are the help pages of the software used by this pipeline.

• multiqc
• nextflow