diff --git a/notebooks/workflow/Flowchart.ipynb b/notebooks/workflow/Flowchart.ipynb
new file mode 100644
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--- /dev/null
+++ b/notebooks/workflow/Flowchart.ipynb
@@ -0,0 +1,390 @@
+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.6.10"
+    },
+    "colab": {
+      "name": "Flowchart.ipynb",
+      "provenance": [],
+      "collapsed_sections": []
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "7uvMRvcz37KB"
+      },
+      "source": [
+        "#!conda install -y -c anaconda pydot \n",
+        "#!conda install -y -c anaconda networkx\n",
+        "\n",
+        "import networkx as nx\n",
+        "import matplotlib.pyplot as plt\n",
+        "import matplotlib.image as mpimg\n",
+        "from io import StringIO\n",
+        "from IPython.display import SVG\n",
+        "import pydot"
+      ],
+      "execution_count": 1,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "juS5DQJu37KG",
+        "outputId": "5af336c7-b631-438c-c676-0b9f20c6bcb7",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 916
+        }
+      },
+      "source": [
+        "dot_graph = pydot.Dot(graph_type='digraph')\n",
+        "\n",
+        "test_bam_node = pydot.Node('Read alignment\\n(BAM)')\n",
+        "test_bam_node.set_shape('box3d')\n",
+        "dot_graph.add_node(test_bam_node)\n",
+        "\n",
+        "test_gem_node = pydot.Node('GEM mappability track\\n(BigWig)')\n",
+        "test_gem_node.set_shape('box3d')\n",
+        "dot_graph.add_node(test_gem_node)\n",
+        "\n",
+        "test_2bit_node = pydot.Node('Reference genome\\n(2BIT)')\n",
+        "test_2bit_node.set_shape('box3d')\n",
+        "dot_graph.add_node(test_2bit_node)\n",
+        "\n",
+        "test_truth_set_vcf_node = pydot.Node('Truth set\\n(VCF)')\n",
+        "test_truth_set_vcf_node.set_shape('box3d')\n",
+        "dot_graph.add_node(test_truth_set_vcf_node)\n",
+        "\n",
+        "test_truth_set_bedpe_node = pydot.Node('Truth set\\n(BEDPE)')\n",
+        "test_truth_set_bedpe_node.set_shape('box3d')\n",
+        "dot_graph.add_node(test_truth_set_bedpe_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_truth_set_vcf_node, test_truth_set_bedpe_node)\n",
+        "iedge.set_label('vcf2bedpe.R')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "clipped_reads_py_node = pydot.Node('clipped_reads.py')\n",
+        "clipped_reads_py_node.set_shape('box')\n",
+        "dot_graph.add_node(clipped_reads_py_node)\n",
+        "\n",
+        "clipped_reads_node = pydot.Node('clipped_reads\\n(JSON.GZ)')\n",
+        "clipped_reads_node.set_shape('box3d')\n",
+        "dot_graph.add_node(clipped_reads_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, clipped_reads_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_reads_py_node, clipped_reads_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "clipped_read_pos_py_node = pydot.Node('clipped_read_pos.py')\n",
+        "clipped_read_pos_py_node.set_shape('box')\n",
+        "dot_graph.add_node(clipped_read_pos_py_node)\n",
+        "\n",
+        "clipped_read_pos_node = pydot.Node('clipped_read_pos\\n(JSON.GZ)')\n",
+        "clipped_read_pos_node.set_shape('box3d')\n",
+        "dot_graph.add_node(clipped_read_pos_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, clipped_read_pos_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_read_pos_py_node, clipped_read_pos_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "split_reads_py_node = pydot.Node('split_reads.py')\n",
+        "split_reads_py_node.set_shape('box')\n",
+        "dot_graph.add_node(split_reads_py_node)\n",
+        "\n",
+        "split_reads_node = pydot.Node('split_reads\\n(JSON.GZ)')\n",
+        "split_reads_node.set_shape('box3d')\n",
+        "dot_graph.add_node(split_reads_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, split_reads_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(split_reads_py_node, split_reads_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "clipped_read_distance_py_node = pydot.Node('clipped_read_distance.py')\n",
+        "clipped_read_distance_py_node.set_shape('box')\n",
+        "dot_graph.add_node(clipped_read_distance_py_node)\n",
+        "\n",
+        "clipped_read_distance_node = pydot.Node('clipped_read_distance\\n(JSON.GZ)')\n",
+        "clipped_read_distance_node.set_shape('box3d')\n",
+        "dot_graph.add_node(clipped_read_distance_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, clipped_read_distance_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_read_distance_py_node, clipped_read_distance_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "coverage_py_node = pydot.Node('coverage.py')\n",
+        "coverage_py_node.set_shape('box')\n",
+        "dot_graph.add_node(coverage_py_node)\n",
+        "\n",
+        "coverage_node = pydot.Node('coverage\\n(NPY.GZ)')\n",
+        "coverage_node.set_shape('box3d')\n",
+        "dot_graph.add_node(coverage_node)\n",
+        "\n",
+        "iedge = pydot.Edge(coverage_py_node, coverage_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "snv_py_node = pydot.Node('snv.py')\n",
+        "snv_py_node.set_shape('box')\n",
+        "dot_graph.add_node(snv_py_node)\n",
+        "\n",
+        "snv_node = pydot.Node('snv\\n(NPY.GZ)')\n",
+        "snv_node.set_shape('box3d')\n",
+        "dot_graph.add_node(snv_node)\n",
+        "\n",
+        "iedge = pydot.Edge(snv_py_node, snv_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "chr_array_py_node = pydot.Node('chr_array.py')\n",
+        "chr_array_py_node.set_shape('box')\n",
+        "dot_graph.add_node(chr_array_py_node)\n",
+        "\n",
+        "chr_array_node = pydot.Node('chr_array\\n(BCOLZ)')\n",
+        "chr_array_node.set_shape('box3d')\n",
+        "dot_graph.add_node(chr_array_node)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_reads_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_read_pos_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(split_reads_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(clipped_read_distance_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(coverage_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(snv_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(test_gem_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(test_2bit_node, chr_array_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(chr_array_py_node, chr_array_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "label_sr_py_node = pydot.Node('label_windows.py')\n",
+        "label_sr_py_node.set_shape('box')\n",
+        "dot_graph.add_node(label_sr_py_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, label_sr_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(split_reads_node, label_sr_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(test_truth_set_bedpe_node, label_sr_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "label_sr_node = pydot.Node('labels\\n(JSON.GZ)')\n",
+        "label_sr_node.set_shape('box3d')\n",
+        "dot_graph.add_node(label_sr_node)\n",
+        "\n",
+        "iedge = pydot.Edge(label_sr_py_node, label_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "create_window_pairs_py_sr_node = pydot.Node('create_window_pairs.py')\n",
+        "create_window_pairs_py_sr_node.set_shape('box')\n",
+        "dot_graph.add_node(create_window_pairs_py_sr_node)\n",
+        "\n",
+        "add_win_channels = pydot.Node('add_win_channels.py')\n",
+        "add_win_channels.set_shape('box')\n",
+        "dot_graph.add_node(add_win_channels)\n",
+        "\n",
+        "train_py_sr_node = pydot.Node('train.py\\n')\n",
+        "train_py_sr_node.set_shape('box')\n",
+        "dot_graph.add_node(train_py_sr_node)\n",
+        "\n",
+        "predict_py_sr_node = pydot.Node('predict.py\\n')\n",
+        "predict_py_sr_node.set_shape('box')\n",
+        "dot_graph.add_node(predict_py_sr_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, label_sr_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(test_truth_set_bedpe_node, label_sr_py_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(label_sr_node, create_window_pairs_py_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(chr_array_node, create_window_pairs_py_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "windows_sr_node = pydot.Node('windows\\n(NPZ)')\n",
+        "windows_sr_node.set_shape('box3d')\n",
+        "dot_graph.add_node(windows_sr_node)\n",
+        "\n",
+        "iedge = pydot.Edge(create_window_pairs_py_sr_node, windows_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "windows_en_node = pydot.Node('windows_en\\n(NPZ)')\n",
+        "windows_en_node.set_shape('box3d')\n",
+        "dot_graph.add_node(windows_en_node)\n",
+        "\n",
+        "iedge = pydot.Edge(test_bam_node, add_win_channels)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(windows_sr_node, add_win_channels)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(add_win_channels, windows_en_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "windows_train_node = pydot.Node('Training set windows_en\\n(NPZ)')\n",
+        "windows_train_node.set_shape('box3d')\n",
+        "dot_graph.add_node(windows_train_node)\n",
+        "\n",
+        "windows_test_node = pydot.Node('Test set windows_en\\n(NPZ)')\n",
+        "windows_test_node.set_shape('box3d')\n",
+        "dot_graph.add_node(windows_test_node)\n",
+        "\n",
+        "model = pydot.Node('Model\\n(HDF5)')\n",
+        "model.set_shape('box3d')\n",
+        "dot_graph.add_node(model)\n",
+        "\n",
+        "iedge = pydot.Edge(windows_train_node, train_py_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(train_py_sr_node, model)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(windows_test_node, predict_py_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(model, predict_py_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "predictions_sr_node = pydot.Node('SV calls\\n(BEDPE)')\n",
+        "predictions_sr_node.set_shape('box3d')\n",
+        "dot_graph.add_node(predictions_sr_node)\n",
+        "\n",
+        "merge_sv_calls = pydot.Node('merge_sv_calls.R')\n",
+        "merge_sv_calls.set_shape('box')\n",
+        "dot_graph.add_node(merge_sv_calls)\n",
+        "\n",
+        "bedpe_to_vcf = pydot.Node('bedpe_to_vcf.py')\n",
+        "bedpe_to_vcf.set_shape('box')\n",
+        "dot_graph.add_node(bedpe_to_vcf)\n",
+        "\n",
+        "predictions_vcf_node = pydot.Node('SV calls\\n(VCF)')\n",
+        "predictions_vcf_node.set_shape('box3d')\n",
+        "dot_graph.add_node(predictions_vcf_node)\n",
+        "\n",
+        "iedge = pydot.Edge(predict_py_sr_node, predictions_sr_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(predictions_sr_node, merge_sv_calls)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(merge_sv_calls, bedpe_to_vcf)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "iedge = pydot.Edge(bedpe_to_vcf, predictions_vcf_node)\n",
+        "iedge.set_label('')\n",
+        "dot_graph.add_edge(iedge)\n",
+        "\n",
+        "dot_graph.write_svg('cnn.svg')\n",
+        "# dot_graph.write_ps2('cnn.ps2')\n",
+        "SVG('cnn.svg')"
+      ],
+      "execution_count": 11,
+      "outputs": [
+        {
+          "output_type": "execute_result",
+          "data": {
+            "text/plain": [
+              "<IPython.core.display.SVG object>"
+            ],
+            "image/svg+xml": "<svg height=\"656pt\" viewBox=\"0.00 0.00 1442.50 656.00\" width=\"1443pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n<g class=\"graph\" id=\"graph0\" transform=\"scale(1 1) rotate(0) translate(4 652)\">\n<title>G</title>\n<polygon fill=\"#ffffff\" points=\"-4,4 -4,-652 1438.5,-652 1438.5,4 -4,4\" stroke=\"transparent\"/>\n<!-- Read alignment\\n(BAM) -->\n<g class=\"node\" id=\"node1\">\n<title>Read alignment\\n(BAM)</title>\n<polygon fill=\"none\" points=\"949.5,-648 846.5,-648 842.5,-644 842.5,-610 945.5,-610 949.5,-614 949.5,-648\" stroke=\"#000000\"/>\n<polyline fill=\"none\" points=\"945.5,-644 842.5,-644 \" stroke=\"#000000\"/>\n<polyline fill=\"none\" points=\"945.5,-644 945.5,-610 \" stroke=\"#000000\"/>\n<polyline fill=\"none\" points=\"945.5,-644 949.5,-648 \" stroke=\"#000000\"/>\n<text fill=\"#000000\" font-family=\"Times,serif\" font-size=\"14.00\" text-anchor=\"middle\" x=\"896\" y=\"-632.8\">Read alignment</text>\n<text fill=\"#000000\" font-family=\"Times,serif\" font-size=\"14.00\" text-anchor=\"middle\" x=\"896\" y=\"-617.8\">(BAM)</text>\n</g>\n<!-- clipped_reads.py -->\n<g class=\"node\" id=\"node6\">\n<title>clipped_reads.py</title>\n<polygon fill=\"none\" points=\"114,-572 0,-572 0,-536 114,-536 114,-572\" stroke=\"#000000\"/>\n<text fill=\"#000000\" font-family=\"Times,serif\" font-size=\"14.00\" text-anchor=\"middle\" x=\"57\" y=\"-550.3\">clipped_reads.py</text>\n</g>\n<!-- Read alignment\\n(BAM)&#45;&gt;clipped_reads.py -->\n<g class=\"edge\" id=\"edge2\">\n<title>Read alignment\\n(BAM)-&gt;clipped_reads.py</title>\n<path d=\"M842.488,-626.5752C694.3487,-619.637 280.0792,-598.6496 123.9699,-572.9164\" fill=\"none\" stroke=\"#000000\"/>\n<polygon fill=\"#000000\" points=\"124.5144,-569.4588 114.0661,-571.2147 123.3289,-576.3577 124.5144,-569.4588\" stroke=\"#000000\"/>\n</g>\n<!-- clipped_read_pos.py -->\n<g class=\"node\" 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+          },
+          "metadata": {
+            "tags": []
+          },
+          "execution_count": 11
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "GUrBkX0N37KK"
+      },
+      "source": [
+        ""
+      ],
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}
\ No newline at end of file
diff --git a/notebooks/workflow/environment.yml b/notebooks/workflow/environment.yml
new file mode 100644
index 00000000..2d3fe604
--- /dev/null
+++ b/notebooks/workflow/environment.yml
@@ -0,0 +1,6 @@
+name: workflow
+channels:
+  - bioconda
+  - r
+  - defaults
+prefix: /Users/lsantuari/Applications/Programming/miniconda3/envs/workflow
diff --git a/notebooks/workflow/readme.md b/notebooks/workflow/readme.md
new file mode 100644
index 00000000..2e1daf12
--- /dev/null
+++ b/notebooks/workflow/readme.md
@@ -0,0 +1,2 @@
+https://mybinder.org/v2/gh/GooglingTheCancerGenome/sv-channels/workflow?filepath=%2Fblob%2Fdev%2Fnotebooks%2FFlowchart.ipynb
+
diff --git a/scripts/utils/collate_calls_cv.sh b/scripts/utils/collate_calls_cv.sh
deleted file mode 100644
index f0d0f567..00000000
--- a/scripts/utils/collate_calls_cv.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bah
-
-for s in DEL INS INV DUP TRA;do
-for c in split_reads gridss manta lumpy delly; do
-
-INPUTDIR=$1/${s}/${c}/
-cat ${INPUTDIR}train_model_with_fit/train_*_test_*_cv*/predictions/cnn_predictions.bedpe | sortBed -i - | awk '{if($1==$4){print $0"\t*\t*\t" $5-$2}else{print $0"\t*\t*\t"0}}' > ${INPUTDIR}cnn_predictions.bedpe
-
-done
-done
diff --git a/scripts/utils/copy_svcallsets.sh b/scripts/utils/copy_svcallsets.sh
deleted file mode 100644
index 59b9c173..00000000
--- a/scripts/utils/copy_svcallsets.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-cp $1/all.vcf $2/all.vcf
-for svcaller in gridss manta lumpy delly; do
-	cp $1/$svcaller\_out/$svcaller.vcf $2/$svcaller\_out/$svcaller.vcf
-done