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A typical command for running the pipeline is:

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

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.