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configuration.md

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Configuring MINI-EX

The config file of MINI-EX is composed by three main sections:

Exectutor scope

MINI-EX is configured to run on a SLURM computer cluster as specified in the executor configuration scope at the top of the config file (to use a different executor, please check the Nextflow documentation). MINI-EX uses a Singularity container built on Docker image with the necessary Python 3.6 modules.

// SPECIFY THE SYSTEM EXECUTOR //
executor {
    name = 'slurm'
    //  --> common examples: local, slurm, sge, azurebatch
    queueSize = 5
}

// SINGULARITY CONTAINERS SETTINGS // (not to be adapted)
process.container = "vibpsb/mini-ex:latest"
singularity {
    enabled = true
    cacheDir = "singularity_cache"
    autoMounts = true
}

name, queueSize and optional settings can be changed according to resource availability.

Params scope

The params section is meant to define parameters and paths that will be used by the pipeline scripts.
The first block defines the paths to the single-cell input files required and provided by the user.

    // INPUT FILES DERIVED FROM SINGLE-CELL DATASETS //
    expressionMatrix = "$baseDir/example/INPUTS/*_matrix.tsv"
    markersOut = "$baseDir/example/INPUTS/*_allMarkers.tsv"
    cellsToClusters = "$baseDir/example/INPUTS/*_cells2clusters.tsv"
    clustersToIdentities = "$baseDir/example/INPUTS/*_identities.tsv"

The second block allows to specify the path to a precomputed GRNBoost2 network. By default, this is set to the GRNBoost2 network of the example run. However, when running MINI-EX for the first time on your own data, grnboostOut should be set to null in order to run GRNBoost2 on your dataset.

    // CACHED FILES // (allows to reuse the initial coexpression network)
    grnboostOut = "/$baseDir/example/OUTPUTS/grnboost2/*_grnboost2.tsv"
    // --> to infer coexpression network de novo, replace the line above by: grnboostOut = null

The third block is composed of paths to species-specific files provided by MINI-EX for supported species.
There are currently four directories, one for each species supported by MINI-EX: Arabidopsis thaliana (data/ath), Oryza sativa (data/osa), Solanum lycopersicum (data/sly) and Zea mays (data/zma).

This consists in:

  • List of known transcription factors of the species.
  • Gene-alias file downloaded from TAIR, funRiceGenes, Sol Genomics Network and MaizeGDB.
  • TF-motif Family file linking each TF to its TF family and reporting wheather direct motif information is available or not, and the motifs directly associated to the TF.
  • Ensemble motif-mapping file obtained by selecting the top motif matches for Cluster Buster and FIMO matches for a collection of motifs mapped to the regulatory regions of the species.
  • Gene-GO links for BP (biological process). For A. thaliana only those supported by experimental evidence ("EXP", "IMP", "IDA", "IPI", "IGI", "IEP") and manually curated ("TAS", "NAS", "IC") are included, while for other species all the evidences are kept. Note: all ancestral terms are included and terms associated with more than 30% of all the genes of the species are filtered out.
    // SPECIES SPECIFIC INFORMATION //
    tfList = "$baseDir/data/ath/ath_TF_list.tsv"
    geneAliases = "$baseDir/data/ath/ath_gene_aliases.tsv"
    // --> if gene aliases are not available, replace the line above by: geneAliases = null 
    infoTf = "$baseDir/data/ath/ath_TF2fam2mot.tsv"
    featureFileMotifs = "$baseDir/data/ath/ath_2021.1_motifMapping.out.gz"
    goFile = "$baseDir/data/ath/ath_full_BP_expcur_ext_names.tsv"
    // --> if GO data is not available, replace the line above by: goFile = null 
    //     (when doing so, termsOfInterest should also be set to <null>)

The fourth block consists of MINI-EX parameters that can be adapted to change the behavior of MINI-EX:

  • When the first parameter doMotifAnalysis is set to false, the motif mapping step in the MINI-EX workflow (step 2) is omitted. This yields less precise GRNs, but allows to run MINI-EX without species-specific information which are only shipped with MINI-EX for supported species.

  • The termsOfInterest parameter is the path to a user-defined file with GO terms of interest. This file should contain terms (e.g. root, phloem, xylem, etc.) related to the process or tissue of interest and will affect the ranking of the final regulons. When set to null, no GO information is taken into account for ranking the regulons and MINI-EX will use its standard ranking procedure.

  • The topMarkers parameter refers to the number of upregulated genes per cluster (sorted by q-value) to use during the cell cluster enrichment. expressionFilter refers to the percentage of cells that need to express the TF to retain the regulon for the specific cell cluster. Default values for both parameters have been chosen by benchmarking different filters against a root gold standard of known protein-DNA interactions.

  • motifFilter can be set to either TF-F_motifs (default) or TF_motifs. The default option keeps regulons in the motif filtering step (step 2) if the regulon is enriched for any motif of that TF family. When setting the parameter to TF_motifs, then only regulons are retained if they are enriched for direct TF-motifs.

  • topRegulons defines the top regulons to show in the two output heatmaps. It can be changed according to the user needs.

  • The enrichmentBackground is the path to a user-defined file containing a list of genes to be used as the background for the enrichment analysis. The file should have one gene id per line. If set to null, the background defaults to the list of genes that are present in the expression matrix.

    // PARAMETERS //
    doMotifAnalysis = true 
    // --> set to <false> if no motif mapping data is available 
    //     [CAUTION: without motif data MINI-EX is less reliable]
    termsOfInterest = "$baseDir/example/INPUTS/GOsIwant.tsv"
    // --> to use the standard ranking procedure, replace the line above by: termsOfInterest = null
    topMarkers = "700"
    expressionFilter = "10"
    motifFilter = "TF-F_motifs" 
    // --> to use the motifs of the TF family: motifFilter = "TF-F_motifs"
    // --> to only use the motifs known for a TF: motifFilter =  "TF_motifs"
    topRegulons = "150"
    enrichmentBackground = null
    // --> to specify an enrichment background: enrichmentBackground = "pathToTheFile", with file containing one gene id per line
    //     (when not specified, the background defaults to the list of genes that are present in the expression matrix)

The last block specifies the output directory.

    // SPECIFY OUTPUT DIRECTORY //
    outputDir = "$baseDir/output"
}

Process scope

The process scope allows the user to define the configuration (memory, parallel environment) for each of the processes run by MINI-EX.
These can be changed according to the resources availabe/needed.

process {
    ...
    withName: run_grnboost {
        memory = '20 GB'
        cpus = 5
    }
    ...
}