Launch pipeline

This tool shows the available parameters for a pipeline in form for you to fill in. It typically works in combination with the nf-core helper package.

Launch a pipeline from the web

Pick a pipeline and release below to show the launch form for that pipeline. When you click Finished, your inputs will be saved and you'll be shown the commands to use to launch the pipeline with your choices.

For more options, such as launching a custom pipeline or using a GitHub branch, please use this tool locally - see below.

Read more about the different nf-core pipelines on the Pipelines page.

Launch a pipeline locally

You can run nf-core launch to submit any pipeline schema to this page and set the parameters required for launch. This should work with any Nextflow pipeline (though the experience is best for pipelines that have a nextflow_schema.json file).

For example, to launch the nf-core/atacseq pipeline in your current directory:

nf-core launch atacseq

To launch your own custom pipeline that you have locally:

nf-core launch ./my_pipeline/

The tool will check the pipeline's schema and create one if none exists, and then ask if you want to use this web tool or the command-line wizard:

$ nf-core launch .

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

    nf-core/tools version 2.3 - https://nf-co.re


INFO    NOTE:This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or profiles

INFO    [✓] Default parameters look match schema validation
INFO    [✓] Pipeline schema looks valid (found 72 params)

Would you like to enter pipeline parameters using a web-based interface or a command-line wizard?

? Choose launch method (Use arrow keys)
 » Web based
   Command line

If you select Web based, then this web page will load with the pipeline parameters for you to fill in. The command-line tool will wait for you to click Finished and then offer to run Nextflow with the supplied parameters.

The command-line wizard uses the exact same procedure, but runs entirely locally with a prompt system. That is best for those running on offline systems, or if you are concerned about sending sensitive information over the web.

The nf-core website stores a cached copy of your answers for 2 weeks under a random ID.