OPTIONS.md

Useful Nextflow options

launch a github hosted project

Use the github repository to launch the execution of a hosted project:

nextflow run SciLifeLab/repository

The github address can also be used:

nextflow run http://github.com/SciLifeLab/Repository

launch a specific version

Use the -r option to launch a specific version based on a tag, branch or commit ID.

nextflow run SciLifeLab/repository -r v1.0

config

More informations on Nextflow documentation. Use the -c option to specify a config file to use.

nextflow run SciLifeLab/repository -c file.config

If no config file is specified, Nextflow will look for $NXF_HOME/config or for nextflow.config in your current directory.

profiles

More informations on Nextflow documentation. A profile can be defined in nextflow.config, includeConfig can be use to include several config files. Example:

profiles {
  milou {
    includeConfig 'configuration/standard.config'
    includeConfig 'configuration/milou.config'
    includeConfig 'configuration/milou-slurm.config'
  }
  bianca {
    includeConfig 'configuration/standard.config'
    includeConfig 'configuration/bianca.config'
    includeConfig 'configuration/bianca-slurm.config'
  }
  milou_interactive {
    includeConfig 'configuration/standard.config'
    includeConfig 'configuration/milou.config'
    includeConfig 'configuration/milou-local.config'
  }
}

clean

Use the clean -f option to remove the files contained in the work directory from the last Nextflow execution.

nextflow clean -f

resume

Use the -resume option to restart the project where it last failed.

nextflow run SciLifeLab/repository -resume

info

Use the info option to get information about the github project.

nextflow info SciLifeLab/repository

pull

Use the pull option to update the github project.

nextflow pull SciLifeLab/repository