Modules

To add a module to ngless there are two options: external or internal modules. External modules are the simplest option.

External modules

External modules can perform two tasks:

  1. Add new references to ngless
  2. Add functions to ngless

Adding references makes them available to the map() call using the reference argument and (optionally) allows for calls to count() without specifying any annotation file.

Like everything else in ngless, these are versioned for reproducibility so that the resulting script implicitly encodes the exact version of the databases used.

Functions in external modules map to command line calls to a script you provide.

How to define an external module

You can use the example module in the ngless source for inspiration. That is a complete, functional module.

A module is defined by an YaML file.

Every module has a name and a version:

name: 'module'
version: '0.0.0'

Everything else is optional.

References

References are added with a references section, which is a list of references. A reference contains a fasta-file and (optionally) a gtf-file. For example:

references:
    -
        name: 'ref'
        fasta-file: 'data/reference.fna'
        gtf-file: 'data/reference.gtf.gz'

Note that the paths are relative to the module directory. The GTF file may be gzipped.

Inialization

An init section defines an initialization command. This will be run before anything else in any script which imports this module. The intention is that the module can check for any dependencies and provide the user with an early error message instead of failing later after. For example:

init:
    init_cmd: './init.sh'
    init_args:
        - "Hello"
        - "World"

will cause ngless to run the command ./init.sh Hello World whenever a user imports the module.

A note about paths: paths you define in the module.yaml file are relative to the Yaml file itself. Thus you put all the necessary scripts and data in the module directory. However, the scripts are run with the current working directory of wherever the user is running the ngless protocol (so that any relative paths that the user specifies work as expected). To find your data files inside your module, ngless sets the environmental variable NGLESS_MODULE_DIR as the path to the module directory.

Functions

To add new functions, use a functions section, which should contain a list of functions encoded in YaML format. Each function has a few required arguments:

nglName the name by which the function will be called inside of an ngless script.

arg0 the script to call for this function. Note that the user will never see this.

For example:

functions:
    -
        nglName: "test"
        arg0: "./run-test.sh"

will enable the user to call a function test() which will translate into a call to the run-test.sh script (see the note above about paths).

You can also add arguments to your function, naturally. Remember that ngless functions can have only one unnamed argument and any number of named arguments. To specify the unnamed argument add a arg1 section, with the key atype (argument type):

        arg1:
            atype: <one of 'readset'/'mappedreadset'/'counts'/'str'/'flag'/'int'/'option'>

The arguments of type readset, mappedreadset, and counts are passed as paths to a file on disk. Your command is assumed to not change these, but make a copy if necessary. Bad things will happen if you change the files. You can specify more details on which kind of file you expect with the following optional arguments:

            filetype: <one of "tsv"/"fq1"/"fq2"/"fq3"/"sam"/"bam"/"sam_or_bam"/"tsv">
            can_gzip: true/false
            can_bzip2: true/false
            can_stream: true/false

The flags can_gzip/can_bzip2 indicate whether your script can accept compressed files (default: False). can_stream indicates whether the input can be a pipe (default: False, which means that an intermediate file will always be used).

For example, if your tool wants a SAM file (and never a BAM file), you can write:

        arg1:
            atype: mappedreadset
            filetype: sam

ngless will ensure that your tool does receive a SAM file (including converting BAM to SAM if necessary).

Finally, additional argument are specified by a list called additional. Entries in this list have exactly the same format as the arg1 entry, except that they have a few extra fields. The extra field name is mandatory, while everything else is optional:

        additional:
            -
                name: <name>
                atype: <as for arg1: 'readset'/'mappedreadset'/...>
                def: <default value>
                required: true/false

Arguments of type flag have an optional extra argument, when-true which is a list of strings which will be passed as extra arguments when the flag is true. You can also just specify a single string. If when-true is missing, ngless will pass an option of the form --name (i.e., a double-dash then the name used). For example:

        additional:
            -
                name: verbose
                atype: bool
                def: false
                when-true: "-v"
            -
                name: complete
                atype: bool
                def: false
                when-true:
                    - "--output=complete"
                    - "--no-filter"

All other argument types are passed to your script using the syntax --name=value if they are present or if a default has been provided.

Arguments of type option map to symbols in ngless and require you to add an additional field allowed specifying the universe of allowed symbols. Ngless will check that the user specifies arguments from the allowable universe. For example:

        additional:
            -
                atype: 'option'
                name: 'verbosity'
                def: 'quiet'
                allowed:
                    - 'quiet'
                    - 'normal'
                    - 'loud'

If you do not have a fixed universe for your argument, then it should be a str argument.

The required flag determines whether the argument is required. Note that arguments with a default argument are automatically optional (ngless may trigger a warning if you mark an argument with a default as required).

To return a value, you must request that ngless generate a new temporary file for the script to generate output to. Therefore, you need to specify a return section, with three parameters: rtype (return type, see below), name the name of the argument to use, and extension the file extension of the output type.

    return:
        rtype: "counts"
        name: "ofile"
        extension: "sam"

rtype must be one of "void", "counts", "readset", or "mappedreadset".

Citation

Finally, if you wish to, you can add a citation:

citation: "A paper which you want to be listed when users import your module"

This will be printed out whenever users use your module and thus will help you get exposure.

Internal Modules

This is very advanced as it requires writing Haskell code which can then interact very deeply with the rest of ngless.

For an example, you can look at the example internal module. If you want to get started, you can ask about details on the ngless user mailing list.