Launch a pipeline

Some Nextflow pipelines have many command line flags. The nf-core pipelines launch command helps you manage these parameters. Choose between a web-based graphical interface or an interactive command-line wizard to enter your pipeline parameters. Both interfaces show documentation alongside each parameter and validate your inputs.

The tool uses the nextflow_schema.json file from a pipeline to provide parameter descriptions, defaults, and grouping. If the pipeline has no schema file, one will be generated automatically at runtime.

Nextflow params variables are saved into a JSON file called nf-params.json and used by Nextflow with the -params-file flag. This makes it easier to reuse your parameters in future runs.

The command takes one argument: either the name of an nf-core pipeline (which will be pulled automatically) or the path to a directory containing a Nextflow pipeline (can be any pipeline, not just nf-core).

nf-core pipelines launch rnaseq -r 3.8.1

Once complete, the wizard will ask if you want to launch the Nextflow run. If not, you can copy and paste the Nextflow command with the nf-params.json file.

INFO     [✓] Input parameters look valid
INFO     Nextflow command:
         nextflow run nf-core/rnaseq -params-file "nf-params.json"
 
 
Do you want to run this command now?  [y/n]:

Launch tool options

  • -r, --revision
    • Specify a pipeline release, branch, or git commit SHA to run
  • -i, --id
    • Use the web GUI for nf-core pipelines by clicking Launch on the website. Once filled in, you will receive an ID to retrieve your inputs with this command.
  • -c, --command-only
    • Specify all parameters directly in the Nextflow command instead of saving them in a JSON file with -params-file.
  • -p, --params-in PATH
    • Supply a nf-params.json file from a previous run to use those values. This will overwrite the pipeline schema defaults before the wizard launches.
  • -o, --params-out PATH
    • Path to save the parameters JSON file. Default: nf-params.json
  • -a, --save-all
    • Save all parameters to the JSON file. By default, the pipeline ignores values that match the schema defaults.
  • -h, --show-hidden
    • Show all parameters, including those marked as hidden. Pipeline schemas can hide rarely used or internal parameters.
  • --url
    • Change the URL for the graphical interface. Useful for website development work.