This workflow performs normalization and batch correction on one or more Skyline documents.
- Start from one or more Skyline documents stored locally or on PanoramaWeb
- Exports precursor and replicate level
.tsv
reports from each document - Combine
.tsv
reports into a singlesqlite
batch database - Perform precursor median normalization and protein DirectLFQ normalization and store normalizaed values in batch database
- Generate an Rmarkdown document which renders to a
.html
batch correction report
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 annotations can be given to specify variabels 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 | ... |
Parameter | Required | Type | Description |
---|---|---|---|
documents |
✅ | Map |
A nested Map of Skyline documents and metadata files with the following syntax: ['<project_1>':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 2 slots. The first has key skyline with the path to the Skyline document, and the second has key metadata with the path to the metadata annotations for the replicates in the 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. |