Launch a pipeline

Some nextflow pipelines have a considerable number of command line flags that can be used. To help with this, you can use the nf-core launch command. You can choose between a web-based graphical interface or an interactive command-line wizard tool to enter the pipeline parameters for your run. Both interfaces show documentation alongside each parameter and validate your inputs.

The tool uses the nextflow_schema.json file from a pipeline to give parameter descriptions, defaults and grouping. If no file for the pipeline is found, one will be automatically generated at runtime.

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

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, doesn’t have to be nf-core).

nf-core launch rnaseq -r 3.8.1

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

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 (or branch / git commit sha) of the project to run
  • -i, --id
    • You can use the web GUI for nf-core pipelines by clicking “Launch” on the website. Once filled in you will be given an ID to use with this command which is used to retrieve your inputs.
  • -c, --command-only
    • If you prefer not to save your inputs in a JSON file and use -params-file, this option will specify all entered params directly in the nextflow command.
  • -p, --params-in PATH
    • To use values entered in a previous pipeline run, you can supply the nf-params.json file previously generated.
    • This will overwrite the pipeline schema defaults before the wizard is launched.
  • -o, --params-out PATH
    • Path to save parameters JSON file to. (Default: nf-params.json)
  • -a, --save-all
    • Without this option the pipeline will ignore any values that match the pipeline schema defaults.
    • This option saves all parameters found to the JSON file.
  • -h, --show-hidden
    • A pipeline JSON schema can define some parameters as ‘hidden’ if they are rarely used or for internal pipeline use only.
    • This option forces the wizard to show all parameters, including those labelled as ‘hidden’.
  • --url
    • Change the URL used for the graphical interface, useful for development work on the website.