Commit d2a7e995 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Merge branch 'frip-optimisation' into dev

parents 38c399b0 76d509e9

.github/workflows/ci.yml

+1 −0
Original line number Diff line number Diff line
@@ -189,6 +189,7 @@ jobs: 
          - verify_output_reporting_skip_igv

          - verify_output_reporting_skip_heatmaps

          - verify_output_reporting_skip_multiqc

          - verify_output_skip_frip

    steps:

      - name: Checkout Code

        uses: actions/checkout@v2

bin/frip.py

+1 −1
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@@ -49,7 +49,7 @@ for idx, bam_file in enumerate(bam_file_list): 


    if first_line is not None:

        print("Calculating " + bam_file + " using " + peak_file_list[idx])

        cr = crpb.CountReadsPerBin([bam_file], bedFile=[peak_file_list[idx]], numberOfProcessors=int(args.threads))

        cr = crpb.CountReadsPerBin([bam_file], bedFile=[peak_file_list[idx]], numberOfProcessors=int(1))



        # Calc the total number of reads in peaks per bam file

        reads_at_peaks = cr.run()

bin/lib/reports.py

+2 −1
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@@ -178,6 +178,7 @@ class Reports: 


        self.frag_hist['group'] = group_short

        self.frag_hist['replicate'] = rep_short

        self.frag_hist = self.frag_hist.reset_index(drop=True)

        self.frag_violin = pd.DataFrame( { "fragment_size" : frags_arr, "group" : group_arr , "replicate": rep_arr} )



    def load_binned_frags(self):
@@ -493,7 +494,7 @@ class Reports: 
        plot_data = self.frag_bin500[self.frag_bin500.columns[-(len(self.frag_bin500.columns)-2):]]

        # plot_data = plot_data.fillna(0)

        corr_mat = plot_data.corr(method='pearson')

        ax = sns.heatmap(corr_mat, annot=True)

        ax = sns.heatmap(corr_mat, annot=True, vmin=0, vmax=1)

        fig.suptitle("Replicate Reproducibility (read counts in 500bp bins)")



        return fig, self.frag_bin500

conf/modules.config

+1 −1
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@@ -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  = [

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