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How to pass extra command-line arguments

Occasionally, a particular project needs to run a particular flavor of a pipeline. How can you adjust pipeline arguments for just this project? You can use looper command extras to solve this problem. Command extras let you pass any string on to the pipeline, which will be appended to the command.

There are 2 ways to use command extras: for sample pipelines, or for project pipelines:

1. Sample pipeline command extras

Adding sample command extras via sample attributes

Looper uses a reserved sample attribute called command_extras, which you can set using general PEP sample modifiers however you wish. For example, if your extras are the same for all samples you could use an append modifier:

    command_extra: "--flavor-flag"

This will add --flavor-flag the end of the command looper constructs. If you need to modulate the extras depending on another attribute value, you could use an imply modifier:

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

Adding sample command extras via the command line

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

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

2. Project pipeline 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.