In metagenomix, five main commands are available:

  create   Write jobs for your pipeline configuration.
  export   Prepare an archive for specific pipeline outputs.
  manage   Edit the contents of your pipeline output folder.
  monitor  Check IO/job status of your pipeline configuration.
  merge    Combine the per-sample outputs into feature tables.

Create

This is the main command to write the scripts of a shotgun metagenomics pipeline, as this is how all the inputs and configuration files are provided by the user, along with other command-line arguments controlling the behaviour of the jobs and whether extra information should be printed to the screen.

Read more about creating all the jobs of a pipeline.

Monitor

This command allows the user to check the progress of the analyses composing a particular pipeline configuration. Therefore, it relies on the exact same inputs and configuration files that were provided by the user for a create command, except those job-related arguments.

Read more about monitoring the progress of a pipeline.

Manage

This command allows the user to move and edit some of the outputs of a particular pipeline configuration, which can be useful because of the amount of files that might be generated and because of the current limitation in terms of output folder naming.

Read more about managing the progress of a pipeline.

Export

This command helps wrapping up the outputs of particular analyses of a pipeline into an archive file (ready for transfer if located on a remote machine). It only relies on an output folder path and software names to focus on.

Read more about exporting the progress of a pipeline.

Merge

This command allows the user to post-process the outputs of some analyses of a particular pipeline configuration. Therefore, it also relies on the exact same inputs and configuration files of a create command, except job-related arguments.

Read more about merging pipeline outputs.