Nextflow usage

The Nextflow command has lot of sub-command to handle workflows. A workflow in Nextflow is called 'project'.

Usage: nextflow [options] COMMAND [arg...]

Options:
  -C
     Use the specified configuration file(s) overriding any defaults
  -D
     Set JVM properties
  -bg
     Execute nextflow in background
  -c, -config
     Add the specified file to configuration set
  -d, -dockerize
     Launch nextflow via Docker (experimental)
  -h
     Print this help
  -log
     Set nextflow log file path
  -q, -quiet
     Do not print information messages
  -syslog
     Send logs to syslog server (eg. localhost:514)
  -v, -version
     Print the program version

Commands:
  clean         Clean up project cache and work directories
  clone         Clone a project into a folder
  cloud         Manage Nextflow clusters in the cloud
  config        Print a project configuration
  console       Launch Nextflow interactive console
  drop          Delete the local copy of a project
  help          Print the usage help for a command
  info          Print project and system runtime information
  kuberun       Execute a workflow in a Kubernetes cluster (experimental)
  list          List all downloaded projects
  log           Print executions log and runtime info
  pull          Download or update a project
  run           Execute a pipeline project
  self-update   Update nextflow runtime to the latest available version
  view          View project script file(s)

To get help on a particular Nextflow subcommand :

nextflow help COMMAND

Exercise 1 :

• Log into a node (with 4G of memory)
• Create one time only the Nextflow directories with script the create_nfx_dirs.sh
• Create directory nextflow-tutorial into your work directory.
• Search last version of Nextflow and load module.
• Execute Nextflow without any parameters. What happened ?
• How many sub command has Nextflow ?
• Get help on run sub-command.
• Load system/Python-3.6.3 to get tldr tool and execute it with "nextflow" as parameter.

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