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Parameters for nf-encyclopedia

The following parameters can be used to customize various aspects of the nf-encyclopedia pipeline. These may either be specified as command line arguments, prefixed with --, or in a new NextFlow configuration file. For example:

pipeline.config
params {
    input = 'input.csv'
    dlib  = 'proteins.dlib'
    fasta = 'proteins.fasta'
}

Input/Output Parameters

  • input (string, required) - A comma-separated values (CSV) file specifying the mass spectrometry data files to be analyzed. This file must have at least two columns: file chrlib. The file columns contains the paths to the mass spectrometry data files in formats supported by MSconvert. The chrlib column contains either true or false depending on whether a file should be considered part of a chromatogram library or not. The optional group maybe used to specify which chromatogram library files should be used to analyze each quantitative run. Optionally, condition and bioreplicate columns can be included and will be used by MSstats. These columns are ignored for chromatogram library files. See the MSstats documentation for details. Here is an example (note that the condition, bioreplicate, and group are optional):

    file chrlib condition bioreplicate group
    lib1.raw true batch1
    lib2.raw true batch2
    trt1.raw false treatment patient1 batch1
    trt2.raw false treatment patient2 batch2
    ctr1.raw false control patient3 batch1
    ctr2.raw false control patient4 batch2

  • dlib (string, required) - A spectral library in EncyclopeDIA’s DLIB format. See the EncyclopeDIA documentation for details.

  • fasta (string, required) - The FASTA containing the subset of proteins sequences for which to search.

  • contrasts (string, required) - The contrast matrix defining the hypothesis tests to perform with MSstats provided as a comma-separated values (CSV) file. The columns of the file should denote conditions from the input CSV file. The first column defines the name of each hypothesis test. See the MSstats documentation for more details. This is an example contrast matrix for the input example above:

    treatment control
    TreatmentVsControl 1 -1

  • result_dir (string) - Where results will be saved. Default: 'results'

  • report_dir (string) - Where reports will be saved. Default: 'reports'
  • mzml_dir (string) - Where mzML files will be saved. Default: 'mzml'
  • email (string) - An email to alert on completion.

Grouping Parameters

  • aggregate (boolean) - Aggregate groups into a single analysis. If true, each group will be searched with EncyclopeDIA separately against their respective chomatogram library. These search results are subsequently aggregated and the false discovery rate (FDR) is estimated for the combined groups. If false, the groups are analyzed individually and FDR is estimated within each group. Default: false

  • agg_name (string) - The file prefix to use for the aggregated data. Default: 'aggregated'

MSconvert Parameters

  • msconvert.demultiplex (boolean) - Demultiplex overlapping DIA windows. Default: true
  • msconvert.force (boolean) - Force existing mzML files to be reconverted. Default false

EncyclopeDIA Parameters

  • encyclopedia.chrlib_suffix (string) - The suffix to append to chromatogram library result files. Default: 'chrlib'

  • encyclopedia.quant_suffix (string) - The suffix to append to quantitative result files. Default 'quant'

  • encyclopedia.args (string) - Command line arguments to pass to all EncyclopeDIA analyses. The default attempts to match the defaults from the EncyclopeDIA graphical user interface. Default: '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window'

  • encyclopedia.local.args (string) - Additional command line arguments to use when searching files. Default: ''

  • encyclopedia.global.args (string) - Additional command line arguments to use when quantifying detected peptides across multiple runs. Default: ''

  • encyclopedia.jar (string) - The location of the EncyclopeDIA executable. Use null if EncyclopeDIA was installed with bioconda. The default is the location in the Docker container. Default: '/code/encyclopedia.jar'

MSstats Parameters

  • msstats.enabled (boolean) - Enable MSstats protein quantification. Default: true

  • msstats.normalization (string) - The normalization method used by MSstats. Must be one of 'equalizeMedians', 'quantile', or 'none'. Default: 'equalizeMedians'

  • msstats.reports (boolean) - Generate MSstats reports. Default: false

Resource Parameters

Change these to reflect your compute environment.

  • max_memory (string) - The maximum memory allowed for each process. Default: '128.GB'
  • max_cpus (integer) - The maximum number of CPUs for each process. Default: 16
  • max_time (string) - The maximum execution time for each process. Default: '240.h'