Versioning
The nf-core/pixelator pipeline is versioned separately from the pixelator command-line tool.
Each release of nf-core/pixelator should use a specific version of pixelator.
Here we explain how to use a different version of nf-core/pixelator among the released ones. And how to use features under development.
Selecting the pipeline version
Nextflow pipelines can easily switch between pipeline versions using the underlying Git version control system. Selecting versions depends on how you run the pipeline.
The easiest option is to use nextflow to fetch and manage pipeline versions.
Updating nf-core/pixelator
nextflow pull nf-core/pixelator
When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it in a cached. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline.
By ensuing you run the latest nf-core/pixelator version, you make sure that you also run the latest pixelator version integrated into the pipeline.
Reproducibility
It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
First, go to the nf-core/pixelator releases page
and find the latest version number - numeric only (eg. 1.3.1).
Then specify this when running the pipeline with -r (one hyphen) - eg. -r 1.3.1.
This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
Using the development version
If you want to run the development version of the nf-core/pixelator pipeline, you can do so by specifying the dev branch.
nextflow run nf-core/pixelator -r dev <the rest of your options...>
If you already have checked out the pipeline once, you can update it with nextflow.
nextflow pull nf-core/nf-core-pixelator
Then, you can run our latest (and under development) version with:
nextflow run nf-core/pixelator -r dev -profile test,docker --outdir results
Overriding pixelator containers
The pipeline is using a pre-configured version of pixelator in all its steps. The nf-core/pixelator pipeline offers a way to override this setting.
It is not recommended to modify the version of pixelator unless it is really needed, for example, to test out a new feature or if you are planning to contribute with code or debug a problem.
Using a version of pixelator different from the default pre-configured can break the pipeline. Use it at your own risk.
--pixelator_container
As most execution profiles will use containers to run the pipeline, the nf-core/pixelator pipeline provides the --pixelator_container
parameter to override the container of pixelator without having to write custom nextflow configuration files.
This flag can be used to override the pixelator container. A container repository URL and a tag must be provided here.
This string will be passed to the container directive of the nextflow modules that use pixelator.
The following example will use the pixelator container version 0.21.2 from Pixelgen Technologies GitHub
instead of the default image available through the BioContainers project on quay.io:
nextflow run nf-core/pixelator --pixelator_container quay.io/pixelgen-technologies/pixelator:0.21.2 --help
Modify the following command with your own parameters in order to use the latest development version of pixelator:
nextflow run nf-core/pixelator --pixelator_container quay.io/pixelgen-technologies/pixelator:dev <other cmd options>