Workflow Parameters

The workflow parameters should be included in a configuration file, an example of which can be found at https://raw.githubusercontent.com/mriffle/nf-skyline-targeted-import/main/resources/pipeline.config

The parameters in this file should be changed to indicate the locations of your data, the options you’d like to use for the software included in the workflow, and the capabilities and configuration for the system on which you are running the workflow steps.

The configuration file is roughly organized as:

params {
...
}

profiles {
...
}

mail {
...
}

The params section includes locations of data and configuration options for a specific run of the workflow.
The profiles sections includes parameters that describe the capabilities of the systems that run the steps of the workflow. For example, if running on your local system, this will include things like how many cores and how much RAM may be used by the steps of the workflow. This will not need to be changed for each run of the workflow.
The mail section includes configuration options for sending email. This is optional and only necessary if you wish to send emails when the workflow completes. This will not need to be changed for each run of the workflow.

Below is a complete description of all parameters that may be included in these sections.

Note

This workflow can process files stored in PanoramaWeb. When specifying directories or file locations, any paths that begin with https:// will be interpreted as being PanoramaWeb locations.

For example, to process raw files stored in PanoramaWeb, you would have the following in your pipeline.config file:

quant_spectra_dir= 'https://panoramaweb.org/_webdav/path/to/@files/RawFiles/'

Where, https://panoramaweb.org/_webdav/path/to/@files/RawFiles/ is the WebDav URL of the folder on the Panorama server.

The `params` Section

Parameters for the `params` section
Req?	Parameter Name	Description
✓	`skyline_template_file`	The Skyline template file used to generate the final Skyline file. This should contain the target peptides or transitions for which to import spectra and calculate quantities. May be local or on PanoramaWeb.
✓	`quant_spectra_dir`	The path to the directory containing the raw data to be quantified. May be local or on PanoramaWeb.
	`quant_spectra_glob`	Which files in this directory to use. Default: `*.raw`
	`import_raw_directly`	If set to `true`, RAW data will be directly imported into Skyline and `msconvert` will not be run. If `false`, `msconvert` is run and the resulting scan data are imported into Skyline. Default: `false`.
	`skyline_document_name`	The base of the file name of the generated Skyline document. If set to `'human_dia'`, the output file name would be `human_dia.sky.zip`. Note: If importing into PanoramaWeb, this is also the name that appears in the list of imported Skyline documents on the project page. Default: `final`.
	`msconvert.do_demultiplex`	If starting with raw files, this is the value used by `msconvert` for the `do_demultiplex` parameter. Default: `true`.
	`msconvert.do_simasspectra`	If starting with raw files, this is the value used by `msconvert` for the `do_simasspectra` parameter. Default: `true`.
	`panorama.upload`	Whether or not to upload results to PanoramaWeb Default: `false`.
	`panorama.upload_url`	The WebDAV URL of a directory in PanoramaWeb to which to upload the results. Note that `panorama.upload` must be set to `true` to upload results.
	`email`	The email address to which a notification should be sent upon workflow completion. If no email is specified, no email will be sent. To send email, you must configure mail server settings (see below).

The `profiles` Section

The example configuration file includes this profiles section:

profiles {

    // "standard" is the profile used when the steps of the workflow are run
    // locally on your computer. These parameters should be changed to match
    // your system resources (that you are willing to devote to running
    // workflow jobs).
    standard {
        params.max_memory = '8.GB'
        params.max_cpus = 4
        params.max_time = '240.h'

        params.mzml_cache_directory = '/data/mass_spec/nextflow/nf-skyline-targeted-import/mzml_cache'
        params.panorama_cache_directory = '/data/mass_spec/nextflow/panorama/raw_cache'
    }
}

These parameters describe the capability of your local computer for running the steps of the workflow. Below is a description of each parameter:

Parameters for the `profiles/standard` section
Req?	Parameter Name	Description
✓	`params.max_memory`	The maximum amount of RAM that may be used by steps of the workflow. Default: 8 gigabytes.
✓	`params.max_cpus`	The number of cores that may be used by the workflow. Default: 4 cores.
✓	`params.max_time`	The maximum amount of a time a step in the workflow may run before it is stopped and error generated. Default: 240 hours.
✓	`params.mzml_cache_directory`	When `msconvert` converts a RAW file to mzML, the mzML file is cached for future use. This specifies the directory in which the cached mzML files are stored.
✓	`params.panorama_cache_directory`	If the RAW files to be processed are in PanoramaWeb, the RAW files will be downloaded to and cached in this directory for future use.

The `mail` Section

This is a more advanced and entirely optional set of parameters. When the workflow completes, it can optionally send an email to the address specified above in the params section. For this to work, the following parameters must be changed to match the settings of your email server. You may need to contact your IT department to obtain the appropriate settings.

The example configuration file includes this mail section:

mail {
    from = 'address@host.com'
    smtp.host = 'smtp.host.com'
    smtp.port = 587
    smtp.user = 'smpt_user'
    smtp.password = 'smtp_password'
    smtp.auth = true
    smtp.starttls.enable = true
    smtp.starttls.required = false
    mail.smtp.ssl.protocols = 'TLSv1.2'
}

Below is a description of each parameter:

Parameters for the `profiles/standard` section
Req?	Parameter Name	Description
✓	`from`	The email address from which the email should be sent.
✓	`smtp.host`	The internet address (host name or ip address) of the email SMTP server.
✓	`smtp.port`	The port on the host to connect to. Most likely will be `587`.
	`smtp.user`	If authentication is required, this is the username.
	`smtp.password`	If authentication is required, this is the password.
✓	`smtp.auth`	Whether or not (true or false) authentication is required.
✓	`smtp.starttls.enable`	Whether or not to enable TLS support.
✓	`smtp.starttls.required`	Whether or not TLS is required.
✓	`smtp.ssl.protocols`	SSL protocol to use for sending SMTP messages.

Workflow Parameters

The params Section

The profiles Section

The mail Section

The `params` Section

The `profiles` Section

The `mail` Section