Commit be0823ec authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Fixed consensus peak threshold bug

parent 4e95724a

conf/modules.config

+1 −1
Original line number Diff line number Diff line
@@ -580,7 +580,7 @@ if(params.run_peak_calling) { 
if(params.run_peak_calling && !params.run_consensus_all) {

    process {

        withName: '.*:CONSENSUS_PEAKS:AWK' {

            ext.command = "' \$10 >= 1 {print \$0}'"

             ext.command = "' \$10 >= " + params.replicate_threshold.toString() + " {print \$0}'"

            ext.ext     = "bed"

            ext.suffix  = ".consensus.peaks.filtered"

            publishDir  = [

nextflow.config

+1 −1
Original line number Diff line number Diff line
@@ -68,7 +68,6 @@ params { 
    // SEACR Peak Calling

    use_control                = true

    peak_threshold             = 0.05

    replicate_threshold        = 1

    only_peak_calling          = false



    // MACS2 Peak Calling
@@ -78,6 +77,7 @@ params { 


    // Consensus Peaks

    consensus_peak_mode        = 'group'

    replicate_threshold        = 1

    skip_upset_plots           = false



    // Reporting and Visualisation

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