Introduction

A typical command for running the pipeline is:

nextflow run nf-core/pixelator \
  -profile docker \
  -params-file <PARAMETER_FILE> \
  --input <SAMPLESHEET> \
  --outdir <OUTPUT_DIRECTORY>

Following placeholders need to be replaced:

• <SAMPLESHEET>: path to a CSV file containing the sample information, including the paths to the input files.
• <PARAMETER_FILE>: path to a YAML file containing the parameters for the pipeline
• <OUTPUT_DIRECTORY>: path to a directory where the results will be saved.

This will launch the pipeline with the docker configuration profile. For other supported profiles, check here.

Read the parameter passing documentation for more information about how to specify parameters. And the output documentation for more information about the output files.

Note that the pipeline will create the following files in your working directory:

work                # Directory containing the nextflow working files
<OUTDIR>            # Finished results in specified location (defined with --outdir)
.nextflow.log       # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.

The following sections deal with the different files and parameters to configure your runs on the nf-core/pixelator pipeline.

📄️ Running the Pipeline

Quick Start

📄️ Samplesheet

Format

📄️ Passing Parameters

Nextflow can pass parameters to the pipeline using both command-line options and through config files.

📄️ Nextflow Parameters

This page gives an overview of Nextflow parameters that can be used to control the pipeline execution.

📄️ Pixelator Parameters

An overview of all parameters available in the nf-core/pixelator pipeline can be viewed in the parameters documentation on nf-co.re

📄️ Configuration

Resources

📄️ Running Offline

The Pixelator pipeline can be executed on systems that are not connected to the internet as Nextflow is able to pre-fetch everything needed to run. There are only two things required in order to prepare for an offline run

📄️ Versioning

The nf-core/pixelator pipeline is versioned separately from the pixelator command-line tool.