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-ms-dda-comet/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:

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
✓	spectra_dir	That path to the location of the raw or mzML files to be processed. This can be a directory location (e.g., /data/mass_spec/my_raw_files/ or a Panorama WebDAV URL (described above).
✓	fasta	That path to the location of the FASTA file to be used in the Comet search. This can be a directory location (e.g., /data/mass_spec/my.fasta or a Panorama WebDAV URL (described above).
	comet_params	That path to the location of the Comet params file to be used in the Comet search. This can be a directory location (e.g., /data/mass_spec/comet.params or a Panorama WebDAV URL (described above). Default: 'comet.params'.
	process_separately	Set to true to run Percolator (and upload to Limelight) separately for each raw file in spectra_dir. This results in a separate Percolator output file and a separate search in Limelight for each raw file. Set to false to combine all Comet results into a single Percolator run and upload all results as a single search (with sub-searches) to Limelight. Setting to false may result in better Percolator statistics, but may make it harder to compare results from individual raw files to results from other searches. Default: false.
	limelight_upload	Set to true to upload to Limelight. If set to true, the following Limelight-related parameters apply. Default: false.
	limelight_project_id	This is required if limelight_upload is set to true. This is the Limelight project ID to which to upload data.
	limelight_webapp_url	This is required if limelight_upload is set to true. This is the URL of the Limelight instance to which to upload data. E.g., 'https://limelight.yeastrc.org/limelight'.
	limelight_search_description	This is required if limelight_upload is set to true. This is a one-line description of the search that will appear in Limelight.
	limelight_search_short_name	This is required if limelight_upload is set to true. This is a very brief one-word nickname for this search. Used in plots to label data.
	limelight_tags	Comma-delimited list of Limelight tags to use for this search (e.g., 'yeast,control,2023'. Any tags present that haven’t been created in Limelight will be created in Limelight. Note: You can also specify categories for tags, and tags with the same tag categories will be grouped together in Limelight. For example, one could have a tag category called treatment and tags called control or irradiated as tags within this tag category. To specify a tag category use the tag category name then a tilda (~) then the tag name. E.g., treatment~control,organism~yeast,year~2023. Default: no tags will be sent.
	limelight_import_decoys	If set to true, decoy hits will be imported into Limelight–enabling target/decoy QC visualization. Only set to true if this is required, dramatically increases file sizes. Default: false
	limelight_entrapment_prefix	If this set, any protein that begins with this string will be considered an entrapment decoy by Limelight–that is a target hit that is secretly really a decoy. This enables some QC/statistic tools within Limelight to estimate error. Example: limelight_entrapment_prefix = 'ENTRAP'. Default: not set.
	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 {
        process.resourceLimits = [ cpus: 4, memory: '8.GB', time: '240.h' ]

        params.mzml_cache_directory = '/data/mass_spec/nextflow/nf-ms-dda-comet/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
✓	process.resourceLimits	A map giving the maximum resources any single step may use: cpus (number of cores), memory (RAM, e.g. '8.GB'), and time (max wall-clock per step before it is stopped, e.g. '240.h'). Every step’s request is automatically capped at these values. Assign the whole map at once — do not split it across separate settings. Defaults: [ cpus: 4, memory: '8.GB', time: '240.h' ].
✓	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 aws profile (AWS Batch)

Run with -profile aws to execute on AWS Batch. In addition to the executor, queue, and S3 cache locations, this profile sets params.aws_region:

Additional parameters for the profiles/aws section

Req?	Parameter Name	Description
✓	params.aws_region	The AWS region of your Batch + Secrets Manager. When downloading from PanoramaWeb or uploading to Limelight on Batch, the API key is bridged through AWS Secrets Manager in this region. See How to Setup and Configure AWS Batch.

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.