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Version: 1.3.x

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: Nextflow itself and any pipeline assets. These have to be set up on an online machine and can be then easily transferred and run offline. Please follow the steps below a the system with internet access:

1. Download the required plugins​

You should already have Nextflow installed on the system with internet access. If this is not the case, go to the Installation section and follow the instructions to install Nextflow.

Start a test run of the pipeline. This step is carried out so Nextflow can download all the plugins required to run the pipeline. It does not need to run to completion.

$ nextflow run nf-core/pixelator -profile test,docker --outdir "./results"

Nextflow will download the pipeline code locally to a specific folder so it can be reused every run.

Find your Nextflow configuration file in that folder and look for the plugins section to specify each plugin that you downloaded, both name and version, including default plugins. This will prevent Nextflow from trying to download newer versions of plugins. We have already pinned most plugins for you in nf-core/pixelator.

2. Download the pipeline assets​

To execute a pipeline offline, it's necessary to have the pipeline's code, its software dependencies, and the shared nf-core/configs configuration profiles. To simplify this process, the nf-core team has developed a utility tool within the nf-core package. This tool is designed to automate the downloading and preparation of these components for offline use. You can use the nf-core tools on the system with internet access to download the pipeline code in an interactive fashion.

$ nf-core download pixelator

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.11.1 - https://nf-co.re
    There is a new version of nf-core/tools available! (2.13.1)


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This tool lets you select the pipeline version and whether you need to download any of the existing institutional configuration files. If using Sigularity, download the containers:

In addition to the pipeline code, this tool can download software containers.
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The pipeline and requirements will be downloaded, configured with their relative paths, and packaged into a .tar.gz file by default.

The process is not automated for Docker images. You will need to download the image, save it to a .tar file which you can then transfer and load on the offline machine.

# Obtain the Docker image
$ docker pull quay.io/biocontainers/pixelator

# Save the image to a .tar file
$ docker save -o path/for/generated/image.tar quay.io/biocontainers/pixelator

3. Transfer everything to the offline system​

Copy the Nextflow binary and $HOME/.nextflow folder to equivalent folders in your offline environment and add the following environment variable to your ~/.bashrc file:

export NXF_OFFLINE='true'

Finally, transfer the .tar.gz file to your offline system and unpack the pipeline files (also containing Singularity images).

If using Docker, transfer the image saved in the previous step and load it using:

$ docker load -i path/to/image.tar

4. Run the pipeline offline​

With all the necessary files in place on the offline environment you should be able to run the pipeline

$ nextflow run <download_directory>/workflow \
    -profile [PROFILE_TO_USE] \
    --input [PATH_TO_SAMPLESHEET] \
    --outdir [OUTPUT_DIRECTORY]