nf-dia-batch-correction

This workflow performs normalization and batch correction on one or more Skyline documents.

Workflow steps

1. Start from one or more Skyline documents stored locally or on PanoramaWeb
2. Exports precursor and replicate level .tsv reports from each document
3. Combine .tsv reports into a single sqlite batch database
4. Perform precursor median normalization and protein DirectLFQ normalization and store normalizaed values in batch database
5. Generate an Rmarkdown document which renders to a .html batch correction report

How to run the workflow

nextflow run -r master uw-maccosslab/nf-dia-batch-correction -c pipeline.config

A template pipeline config is here. The required and optional parameters are described below.

Replicate metadata format

Replicate metadata annotations can be given to specify variables to use in the batch correction report. The metadata files should be .tsv files where the first column has the header Replicate and additional columns for each metadata variable. The values in the Replicate column must match exactly the mzML or raw file names in the Skyline reports.

Replicate	annotationKey1	annotationKey2	...
replicate1	value	value	...
replicate2	value	value	...

Workflow parameters

Parameter	Required	Type	Description
documents	✅	Map	A nested Map of Skyline documents and metadata files with the following syntax: ['<project_1>': ['skyline': '<path_to_skyline_doc>', 'metadata': '<path_to_metadata_tsv>'] ['<project_2>': ['skyline': '<path_to_skyline_doc>', 'metadata': '<path_to_metadata_tsv>'], ... ] There is a slot in the top level Map for each Skyline document. The key is a unique project name for the document. The sub-map should have at least 1 slot. The required slot has key skyline with the path to the Skyline document. Optionally, a second slot with the key metadata is the path to the replicate metadata annotations for the the document. If the metadata key is null or not included, the metadata annotations will be exported from the skyline document. File paths can be local file paths or Panorama WebDav urls.
precursor_report_template		String	Path to precursor quality report template. By default the report template in the resources directory in the git repo is used.
replicate_report_template		String	Path to replicate quality report template. By default the report template in the resources directory in the git repo is used.
normalize_db.exclude_replicates		String, List	Exclude replicate(s) from normalizaton and batch correction. If null, all replicates are included. Default is null.
normalize_db.exclude_projects		String, List	Exclude Skyline document(s) from normalizaton and batch correction. If null, all Skyline documents are included. Default is null.
normalize_db.method		String	Normalization method to use. Available options are DirectLFQ and median. Default is DirectLFQ
bc.method		String	Batch correction method. Either combat or limma. combat is the default.
bc.batch1		String	Metadata key for batch level 1. If null, the project name in documents is used as the batch variable.
bc.batch2		String	Metadata key for batch level 2. A second batch level is only supported with limma as the batch correction method.
bc.color_vars		String, List	Metadata key(s) used to color PCA plots. If null, batch and acquisition number are used to color plots.
bc.covariate_vars		String, List	Metadata key(s) to use as covariates for batch correction. If null, no covariates are used.
bc.control_key		String	Metadata key indicating replicates which are controls for CV plots. If null, all replicates are used in CV distribution plot.
bc.control_values		String	Metadata value(s) mapping to control_key indicating whether a replicate is a control.
bc.plot_ext		String	File extension for standalone plots. If null, no standalone plots are produced.