How to pass extra command-line arguments

Occasionally, a particular project needs to run a particular flavor of a pipeline. We'd like to just adjust the arguments passed for just this project. We may be passing a completely separate config file to the pipeline, or just tweaking a command-line argument. Either way, we treat things the same way.

Looper provides a feature called command extras to solve this problem. Command extras provide a way to pass arbitrary commands through looper on to the pipeline. This extra information can be specified on the command line, or at the sample or project level, depending on the pipeline.

Sample-level command extras

For sample pipelines, there are two possibilities: 1) command line argument for run subcommand and 2) setting sample attribute using general PEP sample modifiers to add a command_extra attribute to any samples, however you wish.

You can pass extra arguments using --command-extra like this:

looper run project_config.yaml --command-extra="--flavor-flag"

For the PEP-based approach, for example, if your extras are the same for all samples you could just use an append modifier:

    command_extra: "--flavor-flag"

Or, if you need to modulate on the basis of some other attribute value, you could use an imply modifier:

    - if:
        protocol: "rrbs"
        command_extra: "-C flavor.yaml --epilog"

Project-level command extras

For project pipelines, you can specify command extras in the looper section of the PEP config:

  output_dir: "/path/to/output_dir"
      command-extra: "--flavor"

or as an argument to the looper runp command:

looper runp project_config.yaml --command-extra="--flavor-flag"

Overriding PEP-based command extras

By default, the CLI extras are appended to the command_extra specified in your PEP. If you instead want to override the command extras listed in the PEP, you can instead use --command-extra-override.

So, for example, make your looper call like this:

looper run --command-extra-override="-R"

That will remove any defined command extras and append -R to the end of any commands created by looper.