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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.

executor {
    name = 'slurm'
    queueSize = 5
}

process.container = "vibpsb/mini-ex:latest"
singularity.enabled = 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 of parameters defines the paths to the input files required and provided by the user.

params {
    expressionMatrix = "$baseDir/example/INPUTS/*_matrix.txt"
    markersOut = "$baseDir/example/INPUTS/*_allMarkers.txt"
    cell2clusters = "$baseDir/example/INPUTS/*_cells2clusters.txt"
    cluster2ident = "$baseDir/example/INPUTS/*_identities.txt"
    TF_list = "$baseDir/example/INPUTS/TF_list.txt"
    termsOfInterest = "$baseDir/example/INPUTS/GOsIwant.txt"
//  termsOfInterest = null

//  grnboostOut = "/$baseDir/example/OUTPUTS/GRNBoost2_output/*_grnboost2.txt"
    grnboostOut = null

The second block of parameters is composed by files provided and necessary for the pipeline to run.
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:

  • 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.
  • 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.
  • 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.
  • Gene-alias file downloaded from TAIR, funRiceGenes, Sol Genomics Network and MaizeGDB.
    doMotifAnalysis = true // set to <false> if no motif mapping data is available [CAUTION: without motif data MINI-EX is less reliable]
    featureFile_motifs = "$baseDir/data/ath/ath_2021.1_motifMapping.out.gz"
    infoTF = "$baseDir/data/ath/ath_TF2fam2mot.txt"
    GOfile = "$baseDir/data/ath/ath_full_BP_expcur_ext_names.txt"
    alias = "$baseDir/data/ath/ath_gene_aliases.txt"

The third block of parameters consists in all the scripts used in the pipeline:

    script_enricher = "$baseDir/bin/enricherv2.4"
    script_checkInput = "$baseDir/bin/MINIEX_checkInput.py"
    script_grnboost = "$baseDir/bin/MINIEX_grnboostMultiprocess.py"
    script_motifs = "$baseDir/bin/MINIEX_filterForMotifs.py"
    script_topDEGs = "$baseDir/bin/MINIEX_selectTopDEGs.py"
    script_expTFs = "$baseDir/bin/MINIEX_filterForTFExp.py"
    script_info = "$baseDir/bin/MINIEX_makeInfoFile.py"
    script_clustermap = "$baseDir/bin/MINIEX_clustermap.py"
    script_networkCentrality = "$baseDir/bin/MINIEX_network_analysis.py"
    script_checkReference = "$baseDir/bin/MINIEX_checkRef.py"
    script_filesEnrichment = "$baseDir/bin/MINIEX_makeFilesEnrichment.py"	
    script_makedfRef = "$baseDir/bin/MINIEX_makeRankingDf_ref.py"
    script_makedfStd = "$baseDir/bin/MINIEX_makeRankingDf_std.py"
    script_makeborda = "$baseDir/bin/MINIEX_makeBorda.py"
    script_scoreEdges = "$baseDir/bin/MINIEX_scoreEdges.py"
    script_heatmapTops = "$baseDir/bin/MINIEX_visual_heatmap_top150.py"
    script_regmaps = "$baseDir/bin/MINIEX_regmap.py"

The last block of parameters defines the filters used along the GRN inference.

The first two filters (tops and expressionFilter) have been chosen by benchmarking different filters against a root gold standard of known protein-DNA interactions.
The first refers to the number of upregulated genes per cluster (sorted by q-value) to use during the cell cluster enrichment, while the second refers to the percentage of cells that need to express the TF to retain the regulon for the specific cell cluster:

  • motifFilter can be set to TF_motifs if the user wishes not to extend the retention of regulons enriched for family motifs, but only to direct TF-motifs
  • topRegs defines the top regulons to show in the two output heatmaps. It can be changed according to the user needs
    tops = "700"
    expressionFilter = "10"
    motifFilter = "TF-F_motifs"	
    topRegs = "150"
}

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
    }
    ...
}