diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py
deleted file mode 100644
index 58cf42ac..00000000
--- a/CRISPRessoReport.py
+++ /dev/null
@@ -1,690 +0,0 @@
-'''
-CRISPResso2 - Kendell Clement and Luca Pinello 2018
-Software pipeline for the analysis of genome editing outcomes from deep sequencing data
-(c) 2020 The General Hospital Corporation. All Rights Reserved.
-'''
-
-import os
-from jinja2 import Environment, FileSystemLoader
-from jinja_partials import generate_render_partial, render_partial
-from CRISPResso2 import CRISPRessoShared
-
-
-def render_template(template_name, jinja2_env, **data):
-    """Render a template with partials.
-
-    Parameters
-    ----------
-    template_name: str
-        The name of the template to render. For example, if you have a template
-        file called `templates/my_template.html` you would pass in
-        `my_template.html`.
-    jinja2_env: jinja2.Environment
-        The Jinja2 environment being used.
-    **data: keyword arguments of any type
-        Additional keyword arguments that are passed to the template.
-
-    Returns
-    -------
-    The rendered template.
-    """
-    def custom_partial_render(partial_template_name, **partial_data):
-        template = jinja2_env.get_template(partial_template_name)
-        partial_data.update(
-            render_partial=generate_render_partial(
-                custom_partial_render,
-            ),
-        )
-        return template.render(**partial_data)
-    return render_partial(
-        template_name, custom_partial_render, **data,
-    )
-
-
-def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT):
-    """
-    Makes an html report for a crispresso run
-
-    Parameters:
-    crispresso_report_file (string): name of the html file to create
-    crispresso_folder (string): path to the crispresso output
-    _ROOT (string): path to crispresso executables (for templates)
-
-    Returns:
-    Nothin
-    """
-    run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder)
-    make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT)
-
-
-def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
-                      amplicon_fig_names, amplicon_figures, crispresso_folder):
-    """
-        Helper function to add figure if the file exists
-        if fig at filename exists,
-        amplicon_figs[figname] is set to that file
-        """
-    # fullpath=os.path.join(crispresso_folder,fig_root+'.png')
-    pngfullpath = os.path.join(crispresso_folder, fig_root + '.png')
-    htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html')
-    #            print('adding file ' + fig_root + ' at ' + fullpath)
-    if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath):
-        amplicon_fig_names.append(fig_name)
-        # amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png')
-        amplicon_figures['locs'][fig_name] = os.path.basename(fig_root)
-        amplicon_figures['titles'][fig_name] = fig_title
-        amplicon_figures['captions'][fig_name] = fig_caption
-        amplicon_figures['datas'][fig_name] = []
-        for (data_caption, data_file) in fig_data:
-            if os.path.exists(os.path.join(crispresso_folder, data_file)):
-                amplicon_figures['datas'][fig_name].append((data_caption, data_file))
-        if os.path.exists(htmlfullpath):
-            with open(htmlfullpath) as html:
-                html_string = "<div align='center'>"
-                html_string += html.read()
-                html_string += "</div>"
-            amplicon_figures['htmls'][fig_name] = html_string
-
-
-def assemble_figs(run_data, crispresso_folder):
-    figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}}
-
-    global_fig_names = []
-    for fig in ['1a', '1b', '1c', '1d', '5a', '6a', '8a', '11c']:
-        fig_name = 'plot_' + fig
-        if fig_name + '_root' in run_data['results']['general_plots']:
-            add_fig_if_exists(fig_name, run_data['results']['general_plots'][fig_name + '_root'], 'Figure ' + fig,
-                              run_data['results']['general_plots'][fig_name + '_caption'],
-                              run_data['results']['general_plots'][fig_name + '_data'],
-                              global_fig_names, figures, crispresso_folder)
-
-    amplicons = []
-    for amplicon_name in run_data['results']['ref_names']:
-        amplicons.append(amplicon_name)
-        amplicon_figures = {'names': [], 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}}
-
-        for fig in ['2a', '3a', '3b', '4a', '4b', '4c', '4d', '4e', '4f', '4g', '5', '6', '7', '8', '10a', '10b', '10c',
-                    '11a']:
-            fig_name = 'plot_' + fig
-            if fig_name + '_root' in run_data['results']['refs'][amplicon_name]:
-                add_fig_if_exists(fig_name, run_data['results']['refs'][amplicon_name][fig_name + '_root'],
-                                  'Figure ' + fig_name,
-                                  run_data['results']['refs'][amplicon_name][fig_name + '_caption'],
-                                  run_data['results']['refs'][amplicon_name][fig_name + '_data'],
-                                  global_fig_names, amplicon_figures, crispresso_folder)
-
-        this_sgRNA_based_fig_names = {}
-        for fig in ['2b', '9', '10d', '10e', '10f', '10g', '11b']:
-            # fig 2b's
-            this_fig_names = []
-            if 'plot_' + fig + '_roots' in run_data['results']['refs'][amplicon_name]:
-                for idx, plot_root in enumerate(run_data['results']['refs'][amplicon_name]['plot_' + fig + '_roots']):
-                    fig_name = "plot_" + fig + "_" + str(idx)
-                    add_fig_if_exists(fig_name, plot_root, 'Figure ' + fig_name + ' sgRNA ' + str(idx + 1),
-                                      run_data['results']['refs'][amplicon_name]['plot_' + fig + '_captions'][idx],
-                                      run_data['results']['refs'][amplicon_name]['plot_' + fig + '_datas'][idx],
-                                      this_fig_names, amplicon_figures, crispresso_folder)
-            this_sgRNA_based_fig_names[fig] = this_fig_names
-
-        figures['names'][amplicon_name] = amplicon_figures['names']
-        figures['sgRNA_based_names'][amplicon_name] = this_sgRNA_based_fig_names
-
-        figures['locs'][amplicon_name] = amplicon_figures['locs']
-        figures['titles'][amplicon_name] = amplicon_figures['titles']
-        figures['captions'][amplicon_name] = amplicon_figures['captions']
-        figures['datas'][amplicon_name] = amplicon_figures['datas']
-        figures['htmls'][amplicon_name] = amplicon_figures['htmls']
-    data = {'amplicons': amplicons, 'figures': figures}
-    return data
-
-
-def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_version=False):
-    # dicts for each amplicon fig_names[amp_name] = [list of fig names]
-    #                        fig_locs[amp_name][fig_name] = figure location
-    #    print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT)
-    data = assemble_figs(run_data, crispresso_folder)
-
-    report_display_name = ""
-    if run_data['running_info']['args'].name != "":
-        report_display_name = run_data['running_info']['args'].name
-
-    # find path between the report and the data (if the report is in another directory vs in the same directory as the data)
-    crispresso_data_path = os.path.relpath(crispresso_folder, os.path.dirname(crispresso_report_file))
-    if crispresso_data_path == ".":
-        crispresso_data_path = ""
-    else:
-        crispresso_data_path += "/"
-
-    report_data = {
-        'amplicons': data['amplicons'],
-        'figures': data['figures'],
-        'run_data': run_data,
-        'report_display_name': report_display_name,
-        'crispresso_data_path': crispresso_data_path,
-    }
-
-    j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')))
-
-    #    dest_dir = os.path.dirname(crispresso_report_file)
-    #    shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir)
-    #    shutil.copy2(os.path.join(_ROOT,'templates','favicon.ico'),dest_dir)
-
-    with open(crispresso_report_file, 'w') as outfile:
-        outfile.write(render_template(
-            'report.html', j2_env, report_data=report_data,
-        ))
-
-
-def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT):
-    batch_names = crispresso2_info['results']['completed_batch_arr']
-    display_names = crispresso2_info['results']['batch_input_names']
-
-    window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names']
-    nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names']
-
-    window_nuc_conv_plots = crispresso2_info['results']['general_plots']['window_nuc_conv_plot_names']
-    nuc_conv_plots = crispresso2_info['results']['general_plots']['nuc_conv_plot_names']
-
-    summary_plot_names = []
-    if 'summary_plot_names' in crispresso2_info['results']['general_plots']:
-        summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names']
-    summary_plot_titles = {}
-    if 'summary_plot_titles' in crispresso2_info['results']['general_plots']:
-        summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles']
-    summary_plot_labels = {}
-    if 'summary_plot_labels' in crispresso2_info['results']['general_plots']:
-        summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels']
-    summary_plot_datas = {}
-    if 'summary_plot_datas' in crispresso2_info['results']['general_plots']:
-        summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas']
-
-    allele_modification_heatmap_plot = {}
-    if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names']
-    else:
-        allele_modification_heatmap_plot['names'] = []
-    if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths']
-    else:
-        allele_modification_heatmap_plot['paths'] = {}
-    if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles']
-    else:
-        allele_modification_heatmap_plot['titles'] = []
-    if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels']
-    else:
-        allele_modification_heatmap_plot['labels'] = {}
-    if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas']
-    else:
-        allele_modification_heatmap_plot['datas'] = {}
-
-    allele_modification_line_plot = {}
-    if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names']
-    else:
-        allele_modification_line_plot['names'] = []
-    if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths']
-    else:
-        allele_modification_line_plot['paths'] = {}
-    if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles']
-    else:
-        allele_modification_line_plot['titles'] = []
-    if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels']
-    else:
-        allele_modification_line_plot['labels'] = {}
-    if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas']
-    else:
-        allele_modification_line_plot['datas'] = {}
-
-    allele_modification_heatmap_plot['htmls'] = {}
-    for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items():
-        with open(heatmap_plot_path) as fh:
-            allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read()
-
-    allele_modification_line_plot['htmls'] = {}
-    for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items():
-        with open(line_plot_path) as fh:
-            allele_modification_line_plot['htmls'][line_plot_name] = fh.read()
-
-    #find path between the report and the data (if the report is in another directory vs in the same directory as the data)
-    crispresso_data_path = os.path.relpath(batch_folder, os.path.dirname(crispressoBatch_report_file))
-    if crispresso_data_path == ".":
-        crispresso_data_path = ""
-    else:
-        crispresso_data_path += "/";
-
-    sub_html_files = {}
-    run_names = []
-    for name in batch_names:
-        display_name = display_names[name]
-        sub_folder = 'CRISPResso_on_' + name
-        crispresso_folder = os.path.join(batch_folder, sub_folder)
-        run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder)
-        if 'running_info' not in run_data:
-            raise Exception('CRISPResso run %s has no report. Cannot add to batch report.' % sub_folder)
-
-        this_sub_html_file = sub_folder + ".html"
-        if run_data['running_info']['args'].place_report_in_output_folder:
-            this_sub_html_file = os.path.join(sub_folder, run_data['running_info']['report_filename'])
-        sub_html_files[display_name] = this_sub_html_file
-
-        run_names.append(display_name)
-
-    output_title = 'CRISPResso Batch Output'
-    if crispresso2_info['running_info']['args'].name != '':
-        output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
-
-    make_multi_report(
-        run_names,
-        sub_html_files,
-        crispressoBatch_report_file,
-        batch_folder,
-        _ROOT,
-        output_title,
-        'batch',
-        summary_plots={
-            'names': summary_plot_names,
-            'titles': summary_plot_titles,
-            'labels': summary_plot_labels,
-            'datas': summary_plot_datas,
-        },
-        window_nuc_pct_quilts=window_nuc_pct_quilts,
-        nuc_pct_quilts=nuc_pct_quilts,
-        window_nuc_conv_plots=window_nuc_conv_plots,
-        nuc_conv_plots=nuc_conv_plots,
-        allele_modification_heatmap_plot=allele_modification_heatmap_plot,
-        allele_modification_line_plot=allele_modification_line_plot,
-    )
-
-
-def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
-    names_arr = crispresso2_info['results']['good_region_names']
-    output_title = 'CRISPResso Pooled Output'
-    if crispresso2_info['running_info']['args'].name != '':
-        output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'pooled')
-
-
-def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
-    names_arr = []
-    output_title = 'CRISPResso Compare Output'
-    if crispresso2_info['running_info']['args'].name != '':
-        output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'compare')
-
-
-def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
-    names_arr = crispresso2_info['meta_names_arr']
-    input_names = crispresso2_info['meta_input_names']
-    output_title = 'CRISPresso Meta Output'
-    if crispresso2_info['running_info']['args'].name != '':
-        output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'meta',
-                                  display_names=input_names)
-
-
-def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
-    names_arr = crispresso2_info['results']['good_region_names']
-    output_title = 'CRISPResso WGS Output'
-    if crispresso2_info['running_info']['args'].name != '':
-        output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'wgs')
-
-
-def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, crispresso_tool,
-                                  display_names=None):
-    """
-    Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled
-
-    Parameters:
-    crispresso2_info (dict): information from the crispresso multi run
-    names_arr (arr of strings): Names of the crispresso runs
-    report_name (string): text to be shown at top of report
-    crispresso_report_file (string): path to write report to
-    folder (string): folder containing crispresso runs
-    _ROOT (string): location of crispresso assets (images, templates, etc)
-    display_names (dict): report_name->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr)
-
-    Returns:
-    Nothin
-    """
-
-    summary_plot_names = []
-    if 'summary_plot_names' in crispresso2_info['results']['general_plots']:
-        summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names']
-    summary_plot_titles = {}
-    if 'summary_plot_titles' in crispresso2_info['results']['general_plots']:
-        summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles']
-    summary_plot_labels = {}
-    if 'summary_plot_labels' in crispresso2_info['results']['general_plots']:
-        summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels']
-    summary_plot_datas = {}
-    if 'summary_plot_datas' in crispresso2_info['results']['general_plots']:
-        summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas']
-
-    run_names = []
-    sub_html_files = {}
-    sub_2a_labels = {}
-    sub_2a_pdfs = {}
-
-    for name in names_arr:
-        display_name = name
-        if display_names is not None:
-            display_name = display_names[name]
-
-        folder_name = 'CRISPResso_on_%s' % name
-        sub_folder = os.path.join(folder, folder_name)
-        run_data = CRISPRessoShared.load_crispresso_info(sub_folder)
-        if 'running_info' not in run_data:
-            raise Exception('CRISPResso run %s has no report. Cannot add to report.' % sub_folder)
-
-        run_names.append(display_name)
-
-        this_sub_html_file = os.path.basename(folder_name) + ".html"
-        if run_data['running_info']['args'].place_report_in_output_folder:
-            this_sub_html_file = os.path.join(os.path.basename(sub_folder), run_data['running_info']['report_filename'])
-        sub_html_files[display_name] = this_sub_html_file
-
-        this_sub_2a_labels = []
-        this_sub_2a_pdfs = []
-        for ref_name in run_data['results']['ref_names']:
-            if 'plot_2a_root' in run_data['results']['refs'][ref_name]:
-                pdf_file = run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf"
-                if os.path.exists(pdf_file):
-                    this_sub_2a_pdfs.append(run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf")
-                    this_sub_2a_labels.append("Nucleotide distribution across " + ref_name)
-
-        sub_2a_labels[display_name] = this_sub_2a_labels
-        sub_2a_pdfs[display_name] = this_sub_2a_pdfs
-
-    make_multi_report(
-        run_names,
-        sub_html_files,
-        crispresso_report_file,
-        folder,
-        _ROOT,
-        report_name,
-        crispresso_tool,
-        summary_plots={
-            'names': summary_plot_names,
-            'titles': summary_plot_titles,
-            'labels': summary_plot_labels,
-            'datas': summary_plot_datas,
-        },
-        )
-
-
-def make_multi_report(
-    run_names,
-    sub_html_files,
-    crispresso_multi_report_file,
-    crispresso_folder,
-    _ROOT,
-    report_name,
-    crispresso_tool,
-    window_nuc_pct_quilts=[],
-    nuc_pct_quilts=[],
-    window_nuc_conv_plots=[],
-    nuc_conv_plots=[],
-    summary_plots={
-        'names': [],
-        'titles': [],
-        'labels': [],
-        'datas': [],
-    },
-    compact_plots_to_show={},
-    allele_modification_heatmap_plot={},
-    allele_modification_line_plot={},
-):
-    """
-    Makes an HTML report for a run containing multiple crispresso runs
-
-    Parameters:
-    run_names (arr of strings): names of runs
-    sub_html_files (dict): dict of run_name->file_loc
-    crispresso_multi_report_file (string): path of file to write to
-    report_name (string): description of report type to be shown at top of report
-    crispresso_folder (string): absolute path to the crispresso output
-    _ROOT (string): absolute path to the crispresso executable
-    summary_plots (dict): a dict with the following keys:
-        names (list): list of plot names - keys for following dicts
-        titles (dict): dict of plot_name->plot_title
-        labels (dict): dict of plot_name->plot_label
-        datas (dict): dict of plot_name->[(datafile_description, data_filename), ...]
-    compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show}
-    allele_modification_heatmap_plot (dict): a dict with the following keys:
-        names (list): list of plot names for heatmaps, keys for dicts below
-        htmls (dict): dict of plot_name->HTML for the plot
-        titles (dict): dict of plot_name->plot_title
-        labels (dict): dict of plot_name->plot_label
-        datas (dict): dict of plot_name->[(datafile_description, data_filename), ...]
-    """
-
-    def dirname(path):
-        return os.path.basename(os.path.dirname(path))
-
-    def fill_default(dictionary, key, default_type=list):
-        if key not in dictionary:
-            dictionary[key] = default_type()
-
-    j2_env = Environment(
-        loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')),
-    )
-    j2_env.filters['dirname'] = dirname
-    if crispresso_tool == 'batch':
-        template = 'batchReport.html'
-    elif crispresso_tool == 'pooled':
-        template = 'pooledReport.html'
-    elif crispresso_tool == 'wgs':
-        template = 'wgsReport.html'
-    else:
-        template = 'multiReport.html'
-
-    crispresso_data_path = os.path.relpath(
-        crispresso_folder, os.path.dirname(crispresso_multi_report_file),
-    )
-    if crispresso_data_path == ".":
-        crispresso_data_path = ""
-    else:
-        crispresso_data_path += "/"
-
-    dictionaries = [
-        allele_modification_heatmap_plot, allele_modification_line_plot,
-    ]
-    keys_and_default_types = [
-        ('names', list),
-        ('htmls', dict),
-        ('titles', list),
-        ('labels', dict),
-        ('datas', dict),
-    ]
-    for dictionary in dictionaries:
-        for key, default_type in keys_and_default_types:
-            fill_default(
-                dictionary,
-                key,
-                default_type,
-            )
-    web = False
-    if not web:
-        for html in sub_html_files:
-            sub_html_files[html] = crispresso_data_path + sub_html_files[html]
-    with open(crispresso_multi_report_file, 'w') as outfile:
-        outfile.write(render_template(
-            template,
-            j2_env,
-            window_nuc_pct_quilts=window_nuc_pct_quilts,
-            nuc_pct_quilts=nuc_pct_quilts,
-            window_nuc_conv_plots=window_nuc_conv_plots,
-            nuc_conv_plots=nuc_conv_plots,
-            crispresso_data_path=crispresso_data_path,
-            report_data={
-                'names': summary_plots['names'],
-                'titles': summary_plots['titles'],
-                'labels': summary_plots['labels'],
-                'datas': summary_plots['datas'],
-                'htmls': [],
-                'crispresso_data_path': crispresso_data_path,
-            },
-            run_names=run_names,
-            sub_html_files=sub_html_files,
-            report_name=report_name,
-            compact_plots_to_show=compact_plots_to_show,
-            allele_modification_heatmap_plot_names=allele_modification_heatmap_plot['names'],
-            allele_modification_heatmap_plot_htmls=allele_modification_heatmap_plot['htmls'],
-            allele_modification_heatmap_plot_titles=allele_modification_heatmap_plot['titles'],
-            allele_modification_heatmap_plot_labels=allele_modification_heatmap_plot['labels'],
-            allele_modification_heatmap_plot_datas=allele_modification_heatmap_plot['datas'],
-            allele_modification_line_plot_names=allele_modification_line_plot['names'],
-            allele_modification_line_plot_htmls=allele_modification_line_plot['htmls'],
-            allele_modification_line_plot_titles=allele_modification_line_plot['titles'],
-            allele_modification_line_plot_labels=allele_modification_line_plot['labels'],
-            allele_modification_line_plot_datas=allele_modification_line_plot['datas'],
-        ))
-
-
-def make_aggregate_report(
-    crispresso2_info,
-    report_name,
-    crispresso_report_file,
-    crispresso_report_folder,
-    _ROOT,
-    folder_arr,
-    crispresso_html_reports,
-    compact_plots_to_show={},
-    display_names=None,
-):
-    """
-    Prepares information to make a report of a CRISPRessoAggregate run
-
-    Parameters:
-    crispresso2_info (dict): information from the crispresso aggregate run
-    report_name (string): text to be shown at top of report
-    crispresso_report_file (string): path to write report to
-    crispresso_report_folder (string): path containing aggregated plots, etc.
-    _ROOT (string): location of crispresso assets (images, templates, etc)
-    folder_arr (arr of strings): paths to the aggregated crispresso folders
-    crispresso_html_reports (dict): folder->html_path; Paths to the aggregated crispresso run html reports
-    compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show}
-    display_names (dict): folder->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr)
-
-    Returns:
-    Nothin
-    """
-    summary_plots = {}
-    if 'summary_plot_names' in crispresso2_info['results']['general_plots']:
-        summary_plots['names'] = crispresso2_info['results']['general_plots']['summary_plot_names']
-    else:
-        summary_plots['names'] = []
-    if 'summary_plot_titles' in crispresso2_info['results']['general_plots']:
-        summary_plots['titles'] = crispresso2_info['results']['general_plots']['summary_plot_titles']
-    else:
-        summary_plots['titles'] = {}
-    if 'summary_plot_labels' in crispresso2_info['results']['general_plots']:
-        summary_plots['labels'] = crispresso2_info['results']['general_plots']['summary_plot_labels']
-    else:
-        summary_plots['labels'] = {}
-    if 'summary_plot_datas' in crispresso2_info['results']['general_plots']:
-        summary_plots['datas'] = crispresso2_info['results']['general_plots']['summary_plot_datas']
-    else:
-        summary_plots['datas'] = {}
-
-    allele_modification_heatmap_plot = {}
-    if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names']
-    else:
-        allele_modification_heatmap_plot['names'] = []
-    if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths']
-    else:
-        allele_modification_heatmap_plot['paths'] = {}
-    if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles']
-    else:
-        allele_modification_heatmap_plot['titles'] = {}
-    if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels']
-    else:
-        allele_modification_heatmap_plot['labels'] = {}
-    if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']:
-        allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas']
-    else:
-        allele_modification_heatmap_plot['datas'] = {}
-
-    allele_modification_line_plot = {}
-    if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names']
-    else:
-        allele_modification_line_plot['names'] = []
-    if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths']
-    else:
-        allele_modification_line_plot['paths'] = {}
-    if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles']
-    else:
-        allele_modification_line_plot['titles'] = {}
-    if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels']
-    else:
-        allele_modification_line_plot['labels'] = {}
-    if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']:
-        allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas']
-    else:
-        allele_modification_line_plot['datas'] = {}
-
-    window_nuc_pct_quilts = []
-    if 'window_nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']:
-        window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names']
-    nuc_pct_quilts = []
-    if 'nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']:
-        nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names']
-
-    run_names = []
-    sub_html_files = {}
-
-    for idx, folder in enumerate(folder_arr):
-        display_name = folder
-        if display_names is not None:
-            display_name = display_names[folder]
-
-        run_names.append(display_name)
-        sub_html_file = os.path.relpath(crispresso_html_reports[folder], crispresso_report_folder)
-        sub_html_files[display_name] = sub_html_file
-
-    for compact_plot in compact_plots_to_show:
-        old_href = compact_plots_to_show[compact_plot]['href']
-        compact_plots_to_show[compact_plot]['href'] = os.path.relpath(old_href, crispresso_report_folder)
-        old_img = compact_plots_to_show[compact_plot]['img']
-        compact_plots_to_show[compact_plot]['img'] = os.path.relpath(old_img, crispresso_report_folder)
-
-    allele_modification_heatmap_plot['htmls'] = {}
-    for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items():
-        with open(heatmap_plot_path) as fh:
-            allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read()
-
-    allele_modification_line_plot['htmls'] = {}
-    for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items():
-        with open(line_plot_path) as fh:
-            allele_modification_line_plot['htmls'][line_plot_name] = fh.read()
-
-    make_multi_report(
-        run_names,
-        sub_html_files,
-        crispresso_report_file,
-        crispresso_report_folder,
-        _ROOT,
-        report_name,
-        window_nuc_pct_quilts=window_nuc_pct_quilts,
-        nuc_pct_quilts=nuc_pct_quilts,
-        summary_plots=summary_plots,
-        compact_plots_to_show=compact_plots_to_show,
-        allele_modification_heatmap_plot=allele_modification_heatmap_plot,
-        allele_modification_line_plot=allele_modification_line_plot,
-    )
diff --git a/templates/CRISPResso_justcup.png b/templates/CRISPResso_justcup.png
deleted file mode 100644
index 3116c48c..00000000
Binary files a/templates/CRISPResso_justcup.png and /dev/null differ
diff --git a/templates/batchReport.html b/templates/batchReport.html
deleted file mode 100644
index d02c6269..00000000
--- a/templates/batchReport.html
+++ /dev/null
@@ -1,163 +0,0 @@
-{% extends "layout.html" %}
-{% block head %}
-<style>
-.nav-tabs.amp-header {
-  border-bottom:none !important;
-}
-
-.card-header.amp-header {
-  border-bottom:none !important;
-}
-.nav-tabs.amp-header .nav-link.active {
-  background-color:lightsteelblue;
-  border-bottom:lightsteelblue;
-}
-
-.tab-content.amp-body {
-  background-color:lightsteelblue;
-}
-
-@media print {
-   .tab-content > .tab-pane {
-    display: block !important;
-    opacity: 1 !important;
-    visibility: visible !important;
-		margin-bottom: 2em !important;
-		page-break-inside: avoid;
-  }
-  .nav-tabs {
-    display:none !important;
-    visibility:hidden !important;
-  }
-  .tab-content.amp-body {
-    background-color:transparent !important;
-  	border:None !important;
-  }
-}
-@media only screen and (max-width: 600px) {
-	.jumbotron img {
-		width:100%
-	}
-}
-</style>
-
-{% endblock %}
-
-{% block content %}
-<div class="row">
-<div class="col-sm-1"></div>
-<div class="col-sm-10">
-
-	<div class="jumbotron" style="background:rgba(0,0,0,0.0); padding:0px" >
-		<div id='jumbotron_content' >
-
-          {% if run_names|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5 id="CRISPResso2_Batch_Output">{{report_name}}</h5>
-              </div>
-              <div class='card-body p-0'>
-                <div class="list-group list-group-flush">
-              {% for run_name in run_names %}
-	      <a href="{{sub_html_files[run_name]}}" class="list-group-item list-group-item-action" id="{{run_name}}">{{run_name}}</a>
-                {% endfor %}
-              </div>
-            </div>
-            </div>
-          {% endif %}
-
-          {% if window_nuc_pct_quilts|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Nucleotide percentages around guides</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in window_nuc_pct_quilts %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if nuc_pct_quilts|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Nucleotide percentages in the entire amplicon</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in nuc_pct_quilts %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if window_nuc_conv_plots|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Conversion of target bases around guides</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in window_nuc_conv_plots %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if nuc_conv_plots|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Conversion of target bases in the entire amplicon</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in nuc_conv_plots %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if report_data['names']|length > 0 %}
-            {% for plot_name in report_data['names'] %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>{{report_data['titles'][plot_name]}}</h5>
-              </div>
-              <div class='card-body'>
-		        {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-              </div>
-            </div>
-            {% endfor %}
-          {% endif %}
-
-
-          </div>
-
-        </div>
-
-		<div align="center" class='p-3'>
-			<a href="/reports_data/{{report_zip_filename}}" class="btn btn-primary" role="button"><i class="fas fa-download"></i> Download report</a>
-			<a href="{{report_path}}" class="btn btn-primary" role="button"><i class="fas fa-link"></i> Link to report</a>
-      <button class='btn btn-primary hidden-print' onclick='window.print();'><i class="fas fa-print"></i> Print</button>
-    </div>
-
-    {# data bit for web version: #}
-    {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
-    #}
-	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
-</div> {# jumbrotron #} <!-- end jumbotron -->
-
-</div> {# column #} <!-- end column -->
-
-<div class="col-sm-1"></div>
-</div>
-{% endblock %}
-
-{% block foot %}
-{% endblock %}
diff --git a/templates/favicon.ico b/templates/favicon.ico
deleted file mode 100644
index 8aed2d07..00000000
Binary files a/templates/favicon.ico and /dev/null differ
diff --git a/templates/layout.html b/templates/layout.html
deleted file mode 100644
index dba520de..00000000
--- a/templates/layout.html
+++ /dev/null
@@ -1,237 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-	<head>
-		<title>CRISPResso2</title>
-		<meta charset="utf-8">
-		<meta name="viewport" content="width=device-width, initial-scale=1">
-		<meta name="description" content="CRISPResso2: Analysis of genome editing outcomes from deep sequencing data">
-		<meta name="author" content="Kendell Clement and Luca Pinello">
-		<link href='https://fonts.googleapis.com/css?family=Montserrat|Ranga:700' rel='stylesheet' type='text/css'>
-        <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap/5.1.3/css/bootstrap.min.css" integrity="sha512-GQGU0fMMi238uA+a/bdWJfpUGKUkBdgfFdgBm72SUQ6BeyWjoY/ton0tEjH+OSH9iP4Dfh+7HM0I9f5eR0L/4w==" crossorigin="anonymous" referrerpolicy="no-referrer" />		<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/fancybox/3.3.5/jquery.fancybox.min.css" />
-		<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.13/css/all.css" integrity="sha384-DNOHZ68U8hZfKXOrtjWvjxusGo9WQnrNx2sqG0tfsghAvtVlRW3tvkXWZh58N9jp" crossorigin="anonymous">
-		<link rel="stylesheet" href="/static/css/main.css">
-
-		<!-- Global site tag (gtag.js) - Google Analytics -->
-		<script async src="https://www.googletagmanager.com/gtag/js?id=UA-136070922-1"></script>
-		<script>
-		 window.dataLayer = window.dataLayer || [];
-		 function gtag(){dataLayer.push(arguments);}
-		 gtag('js', new Date());
-
-		 gtag('config', 'UA-136070922-1');
-		</script>
-
-		<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
-		<script src="https://cdn.plot.ly/plotly-2.11.1.min.js"></script>
-		<style>
-			body {
-				font-family: 'Montserrat', sans-serif !important;
-			{% if current_user is defined %}
-				{% if current_user.is_anonymous or current_user.username != "DEFAULTUSER" %}
-					padding-top:60px;
-				{% endif %}
-			{% endif %}
-			}
-			@media (max-width:1015px)
-			{
-				#crispresso_h
-				{
-					font-size:5rem;
-					font-weight:300;
-					line-height:1.2;
-				}
-				#left_help_div
-				{
-					display:none
-				}
-				#top_help_div
-				{
-					display:block
-				}
-			}
-			@media (min-width:1015px)
-			{
-				#crispresso_h
-				{
-					font-size:8rem;
-					font-weight:300;
-					line-height:1.2;
-				}
-				#left_help_div
-				{
-					display:block
-				}
-				#top_help_div
-				{
-					display:none
-				}
-			}
-		</style>
-
-
-		<!-- Always force latest IE rendering engine (even in intranet) & Chrome Frame
-		Remove this if you use the .htaccess -->
-		<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
-
-		<!-- Replace favicon.ico & apple-touch-icon.png in the root of your domain and delete these references -->
-		{% if current_user is defined %}
-		<link rel="shortcut icon" href="/favicon.ico">
-		{% else %}
-		<link rel="shortcut icon" href="data:image/x-icon;base64,AAABAAEAEBAAAAEAIABoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAQAABILAAASCwAAAAAAAAAAAAD//////////////////////v7+//v7+//7+vr/8/Ly//v6+v/7+/v//v7+/////////////////////////////////////////////v7+///////AwcH/gYSE/3t+fv9+gYD/paWl//39/f/+/v7//v7+/////////////////////////////v7+///////z8/P/hYiI/5adnP+Xn57/lZ6d/42Tk//X19f///////39/f/+/v7///////////////////////39/f//////ury7/5GWlv+psK//nqWk/6Cnpv+osa//kpeW/8rMy//+/v7//////////////////////////////////////5ibm/+orq3/o6mo/5+mpf+gpqT/rLOx/5Wbmf95fnz/oKSj/+7u7v///////v7+///////+/v7///////Hy8v+boKD/s7q5/6yzsf+qsbD/q7Gw/7K5uP+gpqT/mZub/7i7u/+mqan///////7+/v///////v7+///////d3t7/lpyb/5abmv90enn/cXZ2/3N4d/+Ijo7/pKup/4uQj/+Znpz/s7W0///////+/v7///////7+/v//////4+Pj/4aKh/+Ahn//a3Fq/2dtZv9tcmz/i5GK/42Sjv+goaH/5Obl//b29v///////////////////////v7+///////t7u7/1tfW/8nMyf/Ex8T/yczJ/83Qzf/a29r/+fn5///////+/v7/////////////////////////////////+fn5//z8/P/m5ub/9vb2//n5+f/y8vL//f39///////9/f3////////////////////////////4+Pj/5+fn/+np6f//////5OTk/+/v7//k5OT/+vr6/+fn5//l5eX/+vr6//////////////////7+/v//////5ubm//X19f///////f39/+Tk5P//////5eXl//j4+P//////8fHx/+Tk5P///////v7+////////////2dnZ/8nJyf///////////+/v7//IyMj///////Pz8//m5ub///////////+9vb3/09PT////////////+fn5/9DQ0P/39/f////////////c3Nz/sLCw///////7+/v/sLCw//n5+f//////+Pj4/+Hh4f/+/v7/////////////////////////////////8/Pz//X19f///////////8/Pz//o6Oj///////39/f///////////////////////f39///////////////////////+/v7////////////+/v7//v7+/////////////v7+////////////AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==" />
-		{% endif %}
-		<link rel="apple-touch-icon" href="/apple-touch-icon.png">
-
-
-	<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
-	{% block head %}{% endblock %}
-
-	</head>
-
-	<body>
-		{% if current_user is defined %}
-		<div id='left_help_div' style='position:fixed;top:50%;transform:translateY(-50%);left:.1%;width:290px;z-index:99'>
-				{{ self.help_block() }}
-		</div>
-
-		{% with messages = get_flashed_messages(with_categories=true) %}
-		  {% if messages %}
-		    {% for category, message in messages %}
-					{% if category == "error" %}
-					<div class="alert alert-danger alert-dismissible fade show" role="alert">
-						{{ message }}
-						<button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
-					</div>
-					{% else %}
-					<div class="alert alert-warning alert-dismissible fade show" role="alert">
-						{{ message }}
-						<button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
-					</div>
-					{% endif %}
-		    {% endfor %}
-		  {% endif %}
-		{% endwith %}
-		{% endif %}
-
-	{# if default user (normal crispresso mode) #}
-	{% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %}
-
-	<div class="container">
-			<div class="row pb-2">
-				<div class="col-sm-1"></div>
-				{% if current_user is defined %}
-					<div class="col-sm-3 crispresso_cup"> <a href='/'><img class='img-fluid' src="../../../static/imgs/CRISPResso_justcup.png" width="80%"></a>
-				{% else %}
-					<div class="col-sm-3 crispresso_cup"> <a href='https://crispresso2.pinellolab.org'><img class='img-fluid' src="https://crispresso.pinellolab.partners.org/static/imgs/CRISPResso_justcup.png" width="80%"></a>
-				{% endif %}
-					</div>
-				<div class="col-sm-7" >
-					<a href='/' style="text-decoration:none !important; color:rgb(33, 37, 41)"><h1 id='crispresso_h' style="font-family:'Ranga', sans-serif">CRISPResso2 </h1></a>
-					<h3 style="margin-top: -0.5em;padding-right: 2em;">Analysis of genome editing outcomes from deep sequencing data</h3>
-				</div>
-				<div class="col-sm-1">
-				</div>
-			</div>
-
-
-		{% else %}
-			{# if doing user sessions #}
-	<nav class="navbar fixed-top navbar-expand-md bg-light navbar-light">
-  <!-- Brand -->
-  <a class="navbar-brand" href="/">
-{#	<img src="../../../static/imgs/CRISPResso_justcup.png" width="30" height="30" class="d-inline-block align-top" alt="" style="margin-left: 1em;"> #}
-{#		<span style="font-family:'Ranga'">CRISPResso2</span></a> #}
-{{config['BANNER_TEXT']}}</a>
-
-  <!-- Toggler/collapsibe Button -->
-  <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#collapsibleNavbar">
-    <span class="navbar-toggler-icon"></span>
-  </button>
-	<!-- Navbar links -->
-	  <div class="collapse navbar-collapse" id="collapsibleNavbar">
-	    <ul class="navbar-nav ms-auto">
-			{% if not current_user.is_anonymous %}
-				<li class="nav-item">
-					 <a class="nav-link" href="{{url_for('home')}}">
-						<i class="fas fa-user"></i> {{ current_user.username}}
-					</a>
-				</li>
-				<li class="nav-item">
-					 <a class="nav-link" href="{{url_for('home')}}">
-						Home
-					</a>
-				</li>
-			{% endif %}
-			{% block extranavs %}{% endblock %}
-			{% if current_user.role == "Admin" %}
-				 <li class="nav-item">
-					 <a class="nav-link" href="{{url_for('admin.index')}}">Admin</a>
-				 </li>
-			{% endif %}
-			{% if current_user.is_anonymous %}
-				 <li class="nav-item">
-					 <a class="nav-link" href="{{url_for('login')}}">Log in</a>
-				 </li>
-			{% else %}
-				 <li class="nav-item">
-					 <a class="nav-link" href="{{url_for('logout')}}">Logout</a>
-				 </li>
-			{% endif %}
-	    </ul>
-	  </div>
-	</nav>
-	<div class="container">
-	{% endif %}
-
-			<div id='top_help_div'>
-				<div class="row">
-					<div class="col-sm-1" style="margin-right: 4em;"></div>
-					<div class='col-sm-10 pb-2 crispresso_body_div'>
-					{% block help_block %} {% endblock %}
-					</div>
-					<div class="col-sm-1"></div>
-				</div>
-			</div>
-
-			{% block content %}{% endblock %}
-
-			{% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %}
-			<div class="row">
-			<div class="col-sm-1"></div>
-			<footer class="col-sm-10 crispresso_body_div" style='padding-bottom:3em'>
-				<p class="text-center">
-      If you like CRISPResso2 please support us by citing it in your work: <br>
-					Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L.<br>
-					<a href="https://rdcu.be/boxVG" target="_blank">CRISPResso2 provides accurate and rapid genome editing sequence analysis. </a><br>
-					Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026.
-				</p>
-				<p class="text-center"><small> &copy; Copyright <a href="http://pinellolab.org">Kendell Clement and Luca Pinello</a></small></p>
-				<p class="text-center">
-					<small>
-				<a href="https://twitter.com/intent/tweet?text=CRISPResso2%20provides%20accurate%20and%20rapid%20genome%20editing%20sequence%20analysis%20%40kendellclement%20%40lucapinello%20%23CRISPR%20%23CRISPResso2"
-					class="twitter-share-button" data-via="kendellclement" data-size="large" data-count="none" data-hashtags="CRISPR" data-url="http://crispresso2.pinellolab.org">Tweet about CRISPresso2!</a>
-				</small>
-				</p>
-
-			</footer>
-			<div class="col-sm-1"></div>
-		</div>
-		{% else %}
-			<div class="row">
-			<div class="col-sm-1"></div>
-			<footer class="col-sm-10 crispresso_body_div" style='padding-bottom:3em'>
-			  <p class="text-center"><small> &copy; Copyright <a href="http://edilytics.com">Edilytics</a></small></p>
-			</footer>
-			<div class="col-sm-1"></div>
-		</div>
-		{% endif %}
-    </div>
-
-
-			<!-- Optional JavaScript -->
-	    <!-- jQuery first, then Popper.js, then Bootstrap JS -->
-		<script src="https://cdnjs.cloudflare.com/ajax/libs/fancybox/3.3.5/jquery.fancybox.min.js"></script>
-		<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p" crossorigin="anonymous"></script>
-			{% block foot %}{% endblock %}
-	</body>
-
-</html>
diff --git a/templates/multiReport.html b/templates/multiReport.html
deleted file mode 100644
index 8e8d83ca..00000000
--- a/templates/multiReport.html
+++ /dev/null
@@ -1,265 +0,0 @@
-{% extends "layout.html" %}
-{% block head %}
-<style>
-.nav-tabs.amp-header {
-  border-bottom:none !important;
-}
-
-.card-header.amp-header {
-  border-bottom:none !important;
-}
-.nav-tabs.amp-header .nav-link.active {
-  background-color:lightsteelblue;
-  border-bottom:lightsteelblue;
-}
-
-.tab-content.amp-body {
-  background-color:lightsteelblue;
-}
-
-@media print {
-   .tab-content > .tab-pane {
-    display: block !important;
-    opacity: 1 !important;
-    visibility: visible !important;
-		margin-bottom: 2em !important;
-		page-break-inside: avoid;
-  }
-  .nav-tabs {
-    display:none !important;
-    visibility:hidden !important;
-  }
-  .tab-content.amp-body {
-    background-color:transparent !important;
-  	border:None !important;
-  }
-}
-@media only screen and (max-width: 600px) {
-	.jumbotron img {
-		width:100%
-	}
-}
-</style>
-
-{% endblock %}
-
-{% block content %}
-<div class="col-sm-1"></div>
-<div class="col-sm-10">
-
-	<div class="jumbotron" style="background:rgba(0,0,0,0.0); padding:0px" >
-		<div id='jumbotron_content' >
-
-          {% if run_names|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>{{report_name}}</h5>
-              </div>
-              <div class='card-body p-0'>
-                <div class="list-group list-group-flush" style='max-height:80vh;overflow-y:auto'>
-              {% for run_name in run_names %}
-	      <a href="{{report_data['crispresso_data_path']}}{{sub_html_files[run_name]}}" class="list-group-item list-group-item-action">{{run_name}}</a>
-                {% endfor %}
-              </div>
-            </div>
-            </div>
-          {% endif %}
-
-          {% if window_nuc_pct_quilts|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Nucleotide percentages around guides</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in window_nuc_pct_quilts %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if nuc_pct_quilts|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Nucleotide percentages in the entire amplicon</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in nuc_pct_quilts %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if window_nuc_conv_plots|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Conversion of target bases around guides</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in window_nuc_conv_plots %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if nuc_conv_plots|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Conversion of target bases in the entire amplicon</h5>
-              </div>
-              <div class='card-body'>
-                {% for plot_name in nuc_conv_plots %}
-                    <h5>{{report_data['titles'][plot_name]}}</h5>
-		            {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-                {% endfor %}
-              </div>
-            </div>
-          {% endif %}
-
-          {% if report_data['names']|length > 0 %}
-            {% for plot_name in report_data['names'] %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>{{report_data['titles'][plot_name]}}</h5>
-              </div>
-              <div class='card-body' style='max-height:80vh;overflow-y:auto'>
-		        {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-              </div>
-            </div>
-            {% endfor %}
-          {% endif %}
-
-          {% if allele_modification_heatmap_plot_names|length > 0 %}
-            {% for heatmap_plot_name in allele_modification_heatmap_plot_names %}
-              {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %}
-              {% set modification_type = heatmap_plot_name.split('_')[3] %}
-              <div class="card text-center mb-2">
-                <div class="card-header">
-                    <h5>{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}</h5>
-                    <ul class="nav nav-tabs justify-content-center card-header-tabs" id="aln-tab" role="tablist">
-                        <li class="nav-item" role="presentation">
-                            <a class="nav-link active" data-bs-toggle="tab" id="{{modification_type}}-heatmap-tab" data-bs-target="#{{heatmap_plot_name}}" role="tab" aria-controls="{{heatmap_plot_name}}" aria-selected="true">Heatmap</a>
-                        </li>
-                        <li class="nav-item" role="presentation">
-                            <a class="nav-link" data-bs-toggle="tab" id="{{modification_type}}-line-tab" data-bs-target="#{{line_plot_name}}" role="tab" aria-controls="{{line_plot_name}}" aria-selected="false">Line</a>
-                        </li>
-                    </ul>
-                </div>
-                <div class="card-body">
-                    <div class="tab-content" id="allele-modification-{{modification_type}}-tabs">
-                        <div class="tab-pane fade show active" id="{{heatmap_plot_name}}" role="tabpanel" aria-labelledby="{{modification_type}}-heatmap-tab">
-                            {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}}
-                            <label class="labelpadding">{{allele_modification_heatmap_plot_labels[heatmap_plot_name]}}</label>
-                            {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %}
-                                <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-                            {% endfor %}
-                        </div>
-                        <div class="tab-pane fade" id="{{line_plot_name}}" role="tabpanel" aria-labelledby="{{modification_type}}-line-tab">
-                            {{allele_modification_line_plot_htmls[line_plot_name]}}
-                            <label class="labelpadding">{{allele_modification_line_plot_labels[line_plot_name]}}</label>
-                            {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %}
-                                <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-                            {% endfor %}
-                        </div>
-                    </div>
-                </div>
-              </div>
-              <script type="application/javascript">
-               document.addEventListener("DOMContentLoaded", () => {
-                   $("#{{modification_type}}-heatmap-tab").on("shown.bs.tab", (e) => {
-                       let plot = document.getElementById("allele-modification-heatmap-{{modification_type}}");
-                       Plotly.Plots.resize(plot);
-                       window.dispatchEvent(new Event("resize"));
-                   });
-                   $("#{{modification_type}}-line-tab").on("shown.bs.tab", (e) => {
-                       let plot = document.getElementById("allele-modification-line-{{modification_type}}");
-                       Plotly.Plots.resize(plot);
-                       window.dispatchEvent(new Event("resize"));
-                   });
-               });
-              </script>
-            {% endfor %}
-              <!-- The below code is another failed attempt to make the heatmaps go fullscreen.
-                   To implement this behavior, wrap the `allele_modification_heatmap_plot_htmls[plot_name]` in a `div`
-                   of class `plotly-full-screen`. -->
-              <!-- <style>
-                   .plot-zoom {
-                   position: absolute;
-                   border: none;
-                   background-color: transparent;
-                   bottom: 0;
-                   right: 0;
-                   }
-                   .full-screen {
-                   position: fixed;
-                   height: 98vh !important;
-                   width: 98vw !important;
-                   left: 0;
-                   top: 0;
-                   z-index: 9999;
-                   overflow: hidden;
-                   }
-                   </style> -->
-              <!-- <script type="application/javascript">
-                   const plotZoom = (el) => {
-                   el = $(el);
-                   let parent = el.parent().parent();
-                   if (el.attr("data-full_screen") === "false") {
-                   parent.addClass("full-screen").trigger("resize").fadeOut().fadeIn();
-                   el.attr("data-full_screen", "true");
-                   Plotly.Plots.resize(parent.find(".plotly-graph-div")[0]);
-                   } else {
-                   parent.removeClass("full-screen").trigger("resize").fadeOut().fadeIn();
-                   el.attr("data-full_screen", "false");
-                   Plotly.Plots.resize(parent.find(".plotly-graph-div")[0]);
-                   }
-                   }
-                   document.addEventListener("DOMContentLoaded", () => {
-                   $(function() {
-                   $(".plotly-full-screen").append(`
-                   <div style="position: relative;">
-                   <button onclick=plotZoom(this) class="plot-zoom" data-full_screen="false" title="Full Screen">
-                   <i class="fa fa-expand-arrows-alt"></i>
-                   </button>
-                   </div>
-                   `);
-                   });
-                   });
-                   </script> -->
-          {% endif %}
-
-          {% if compact_plots_to_show|length > 0 %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>Summary Plots</h5>
-              </div>
-              <div class='card-body p-0'>
-                <div class="list-group list-group-flush" style='max-height:80vh;overflow-y:auto'>
-							  {% for compact_plot in compact_plots_to_show %}
-	      <a href="{{report_data['crispresso_data_path']}}{{compact_plots_to_show[compact_plot]['href']}}" data-toggle="tooltip" title="{{compact_plot}}" class="list-group-item list-group-item-action p-0"><img src="{{report_data['crispresso_data_path']}}{{compact_plots_to_show[compact_plot]['img']}}" width='100%' ></a>
-                {% endfor %}
-              </div>
-              </div>
-            </div>
-          {% endif %}
-
-
-          </div>
-
-        </div>
-
-	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
-</div> {# jumbrotron #} <!-- end jumbotron -->
-
-</div> {# column #} <!-- end column -->
-
-<div class="col-sm-1"></div>
-{% endblock %}
-
-{% block foot %}
-{% endblock %}
diff --git a/templates/pooledReport.html b/templates/pooledReport.html
deleted file mode 100644
index f4550e82..00000000
--- a/templates/pooledReport.html
+++ /dev/null
@@ -1,101 +0,0 @@
-{% extends "layout.html" %}
-{% block head %}
-<style>
-.nav-tabs.amp-header {
-  border-bottom:none !important;
-}
-
-.card-header.amp-header {
-  border-bottom:none !important;
-}
-.nav-tabs.amp-header .nav-link.active {
-  background-color:lightsteelblue;
-  border-bottom:lightsteelblue;
-}
-
-.tab-content.amp-body {
-  background-color:lightsteelblue;
-}
-
-@media print {
-   .tab-content > .tab-pane {
-    display: block !important;
-    opacity: 1 !important;
-    visibility: visible !important;
-		margin-bottom: 2em !important;
-		page-break-inside: avoid;
-  }
-  .nav-tabs {
-    display:none !important;
-    visibility:hidden !important;
-  }
-  .tab-content.amp-body {
-    background-color:transparent !important;
-  	border:None !important;
-  }
-}
-@media only screen and (max-width: 600px) {
-	.jumbotron img {
-		width:100%
-	}
-}
-</style>
-
-{% endblock %}
-
-{% block content %}
-<div class="row">
-<div class="col-sm-1"></div>
-<div class="col-sm-10">
-
-	<div class="jumbotron" style="background:rgba(0,0,0,0.0); padding:0px" >
-		<div id='jumbotron_content' >
-
-            {% if run_names|length > 0 %}
-            <div class='card text-center mb-2'>
-                <div class='card-header'>
-                    <h5>{{report_name}}</h5>
-                </div>
-                <div class='card-body p-0'>
-                    <div class="list-group list-group-flush">
-                        {% for region_name in run_names %}
-	                    <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action">{{region_name}}</a>
-                        {% endfor %}
-                    </div>
-                </div>
-            </div>
-            {% endif %}
-
-          {% if report_data['names']|length > 0 %}
-            {% for plot_name in report_data['names'] %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5 id="modification_summary_title">{{report_data['titles'][plot_name]}}</h5>
-              </div>
-              <div class='card-body' style='max-height:80vh;overflow-y:auto'>
-                  {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-              </div>
-            </div>
-            {% endfor %}
-          {% endif %}
-
-           	<div align="center" class='p-3'>
-			     <a href="/reports_data/{{report_zip_filename}}" class="btn btn-primary" role="button"><i class="fas fa-download"></i> Download report</a>
-			     <a href="{{report_path}}" class="btn btn-primary" role="button"><i class="fas fa-link"></i> Link to report</a>
-                 <button class='btn btn-primary hidden-print' onclick='window.print();'><i class="fas fa-print"></i> Print</button>
-            </div>
-    {# data bit for web version: #}
-    {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
-    #}
-	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
-</div> {# jumbrotron #} <!-- end jumbotron -->
-
-</div> {# column #} <!-- end column -->
-
-<div class="col-sm-1"></div>
-</div>
-{% endblock %}
-
-{% block foot %}
-{% endblock %}
diff --git a/templates/report.html b/templates/report.html
deleted file mode 100644
index fb755d18..00000000
--- a/templates/report.html
+++ /dev/null
@@ -1,693 +0,0 @@
-{% extends "layout.html" %}
-{% block head %}
-<style>
-.nav-tabs.amp-header {
-  border-bottom:none !important;
-}
-
-.card-header.amp-header {
-  border-bottom:none !important;
-}
-.nav-tabs.amp-header .nav-link.active {
-  background-color:lightsteelblue;
-  border-bottom:lightsteelblue;
-}
-
-.pre-scrollable {
-    max-height: 340px;
-    overflow-y: auto;
-    background-color: #f8f8f8;
-    text-align: left
-}
-
-.tab-content.amp-body {
-  background-color:lightsteelblue;
-}
-
-@media print {
-   .tab-content > .tab-pane {
-    display: block !important;
-    opacity: 1 !important;
-    visibility: visible !important;
-		margin-bottom: 2em !important;
-		page-break-inside: avoid;
-  }
-  .nav-tabs {
-    display:none !important;
-    visibility:hidden !important;
-  }
-  .tab-content.amp-body {
-    background-color:transparent !important;
-  	border:None !important;
-  }
-}
-@media only screen and (max-width: 600px) {
-	.jumbotron img {
-		width:100%
-	}
-}
-</style>
-
-{% endblock %}
-
-{% block content %}
-<div class="col-sm-1"></div>
-<center><div class="col-sm-10">
-	<div class="jumbotron h-100 p-5 rounded-3" style="background:rgba(0,0,0,0.0); padding:0px" >
-		<div id='jumbotron_content' >
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					{% if report_data['report_display_name'] != '' %}
-					<h5>{{report_data['report_display_name']}}</h5>
-					{% endif %}
-					<h5>CRISPResso2 run information</h5>
-					<ul class="nav nav-tabs justify-content-center card-header-tabs" id="log-tab" role="tablist">
-						<li class="nav-item">
-						<button class="nav-link active" id="log_aln-tab" data-bs-toggle="tab" data-bs-target="#log_aln" role="tab" aria-controls="log_aln" aria-selected="true">Alignment statistics</button>
-						</li>
-						<li class="nav-item">
-						<button class="nav-link" id="log_params-tab" data-bs-toggle="tab" data-bs-target="#log_params" role="tab" aria-controls="log_params" aria-selected="false">Run Parameters</button>
-						</li>
-					</ul>
-				</div>
-				<div class='card-body'>
-					<div class='tab-content'>
-						<div class="tab-pane fade show active" id="log_aln" role="tabpanel">
-							{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a')}}
-						</div>
-						{{ render_partial('shared/partials/log_params.html', report_data=report_data) }}
-					</div>
-				</div>
-			</div>
-
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					<h5>Allele assignments</h5>
-					<ul class="nav nav-tabs justify-content-center card-header-tabs" id="aln-tab" role="tablist">
-						<li class="nav-item">
-							<button class="nav-link active" id="aln_pie-tab" data-bs-toggle="tab" data-bs-target="#aln_pie" role="tab" aria-controls="aln_pie" aria-selected="true">Piechart</button>
-						</li>
-						<li class="nav-item">
-							<button class="nav-link" id="aln_bar-tab" data-bs-toggle="tab" data-bs-target="#aln_bar" role="tab" aria-controls="aln_bar" aria-selected="false">Barplot</button>
-						</li>
-    						{% if report_data['figures']['locs']['plot_1d'] %}
-						<li class="nav-item">
-							<button class="nav-link" id="aln_dsODN-tab" data-bs-toggle="tab" data-bs-target="#aln_dsODN" role="tab" aria-controls="aln_dsODN" aria-selected="false">dsODN</button>
-						</li>
-              			{% endif %}
-					</ul>
-				</div>
-				<div class='card-body'>
-					<div class="tab-content" id="tabContent">
-						<div class="tab-pane fade show active" id="aln_pie" role="tabpanel" aria-labelledby="aln_pie-tab">
-							{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b')}}
-						</div>
-						<div class="tab-pane fade" id="aln_bar" role="tabpanel" aria-labelledby="aln_bar-tab">
-							{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c')}}
-						</div>
-    						{% if report_data['figures']['locs']['plot_1d'] %}
-						<div class="tab-pane fade" id="aln_dsODN" role="tabpanel" aria-labelledby="aln_dsODN-tab">
-							{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d')}}
-						</div>
-              			{% endif %}
-					</div>
-				</div>
-			</div> {# end card #}
-
-        		{# start global coding sequence report #}
-			{% if report_data['figures']['locs']['plot_5a'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					<h5>Global frameshift analysis</h5>
-				</div>
-				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a')}}
-				</div>
-			</div>
-			{% endif %}
-
-			{% if report_data['figures']['locs']['plot_6a'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					<h5>Global frameshift mutagenesis profiles</h5>
-				</div>
-				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a')}}
-				</div>
-			</div>
-			{% endif %}
-
-			{% if report_data['figures']['locs']['plot_8a'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					<h5>Global splicing analysis</h5>
-				</div>
-				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}}
-				</div>
-			</div>
-			{% endif %}
-			{# end of global coding sequence analysis #}
-
-			{# start hdr summary #}
-			{% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-					<h5>HDR summary plot</h5>
-					{% else %}
-					<h5>HDR summary report (all reads aligned to {{report_data.amplicons[0]}})</h5>
-					{% endif %}
-				</div>
-				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}}
-				</div>
-			</div>
-			{% endif %}
-            		{# end HDR summary #}
-
-			{# start prime editing report #}
-			{% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-					<h5>Prime editing report</h5>
-					{% else %}
-  					<h5>Prime editing report (all reads aligned to {{report_data.amplicons[0]}})</h5>
-					{% endif %}
-				</div>
-  				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}}
-				</div>
-			</div>
-			{% endif %}
-
-			{% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and  report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-					{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-					<h5>Prime editing summary plots at analysis positions</h5>
-					{% else %}
-  					<h5>Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})</h5>
-					{% endif %}
-				</div>
-				<div class='card-body'>
-					{% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %}
-					<div class='mb-4'>
-						{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}}
-					</div>
-					{% endfor %}
-				</div>
-			</div>
-			{% endif %}
-			{# end plot 11b for prime editing #}
-
-			{% if report_data['figures']['locs']['plot_11c'] %}
-			<div class='card text-center mb-2'>
-				<div class='card-header'>
-  					<h5>Scaffold insertions</h5>
-				</div>
-  				<div class='card-body'>
-					{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}}
-				</div>
-			</div>
-			{% endif %}
-			{# end prime editing section #}
-
-			{% if report_data.amplicons|length == 1 %}
-          	<div> {# if only one amplicon, just a normal div #}
-          	{% else %}
-	        {# If there is more than one amplicon, print a navigation to show each amplicon #}
-			<p>Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:</p>
-			<div id='amplicons-card' class='card text-center mb-2'>
-				<div class='card-header amp-header'>
-					<h5>Amplicons</h5>
-					<ul class="nav nav-tabs amp-header card-header-tabs" id="nav-tab" role="tablist">
-					{% for amplicon_name in report_data.amplicons %}
-						{% if loop.index0 == 0 %}
-						<li class="nav-item">
-							<button class="nav-link active" id="pills_{{amplicon_name}}_tab" data-bs-toggle="tab" data-bs-target="#div_{{amplicon_name}}" role="tab" aria-controls="div_{{amplicon_name}}" aria-selected="true">{{amplicon_name}}</button>
-						</li>
-						{% else %}
-						<li class="nav-item">
-							<button class="nav-link" id="pills_{{amplicon_name}}_tab" data-bs-toggle="tab" data-bs-target="#div_{{amplicon_name}}" role="tab" aria-controls="div_{{amplicon_name}}" aria-selected="false">{{amplicon_name}}</button>
-						</li>
-						{% endif%}
-					{% endfor %}
-					</ul>
-				</div>
-				{% endif %} {# end if report contains more than one amplicon #}
-
-
-				{% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #}
-				<div>
-				{% else %}
-				<div class="tab-content pt-3 pr-3 pl-3 amp-body card-body" id="nav-tabContent">
-				{% endif %}
-
-				{% for amplicon_name in report_data.amplicons %}
-					{% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #}
-					<div>
-					{% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #}
-					<div class="tab-pane fade show active" id="div_{{amplicon_name}}" role="tabpanel" aria-labelledby="pills_{{amplicon_name}}_tab">
-            			<div class="d-none d-print-block"><h3>Reads aligning to {{amplicon_name}}</h3></div> {# this bit appears in print mode #}
-					{% else %} {# otherwise inactive tab #}
-					<div class="tab-pane fade" id="div_{{amplicon_name}}" role="tabpanel" aria-labelledby="pills_{{amplicon_name}}_tab">
-            			<div class="d-none d-print-block"><h3>Reads aligning to {{amplicon_name}}</h3> </div>{# this bit appears in print mode #}
-							{% endif %}
-
-		      				<div class='card text-center mb-2'>
-      							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-      								<h5>Nucleotide composition</h5>
-								{% else %}
-      								<h5>Nucleotide composition for {{amplicon_name}}</h5>
-								{% endif %}
-      							</div>
-      							<div class='card-body'>
-								{% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %}
-								<div class='div_zoom_outer d-none d-md-block' style="height:100px;border:1px solid #DDDDDD;position:relative">
-									<div id="zoomview_nucs_{{amplicon_name}}" style="position:absolute;left:0;height:100%;width:100%;background-image: url({{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name]['plot_2a']}}.png);background-size:auto 100%;background-repeat:no-repeat;"></div>
-  										<div class="d-lg-none" style="overflow-x:scroll;overflow-y:hidden;position:absolute;width:100%;height:100%">
-	  										<img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name]['plot_2a']}}.png" style='height:100%'>
-  										</div>
-								</div>
-									<div style='position:relative;display:inline-block;width:95%'>
-										<a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name]['plot_2a']}}.pdf">
-    									<div id='zoomlens_nucs_{{amplicon_name}}' class="d-none d-lg-block" style='float: left;position: absolute;left: 0px;top: 0px;z-index: 1000;border: 1px solid #DDDDDD;height:100%;width:10%'></div>
-    										<img id='tozoom_nucs_{{amplicon_name}}' src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name]['plot_2a']}}.png" width='100%' style='position:relative'></a>
-										</div>
-										<label class="labelpadding">
-  										<span class='d-none d-md-block'>Hover your mouse over the bottom image to zoom in on a specific region.</span><br>
-  											{{report_data['figures']['captions'][amplicon_name]['plot_2a']}}
-										</label>
-							  			{% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %}
-							  			<p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-                						{% endfor %}
-								{% endif %}
-
-								{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and  report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%}
-  									{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %}
-									{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}}
-  									{% endfor %}
-								{% endif %}
-            		</div>
-					</div> {# end card #}
-
-  						<div class='card text-center mb-2'>
-  							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-      							<h5>Modification lengths</h5>
-								{% else %}
-      							<h5>Modification lengths for {{amplicon_name}}</h5>
-								{% endif %}
-  								<ul class="nav nav-tabs justify-content-center card-header-tabs" id="aln-tab" role="tablist">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link active" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_3a" role="tab" aria-controls="{{amplicon_name}}_3a" aria-selected="true">Summary</button>
-  						  			</li>
-            								{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_3b" role="tab" aria-controls="{{amplicon_name}}_3b" aria-selected="false">Indels</button>
-  						  			</li>
-            						{% endif %}
-  								</ul>
-  							</div>
-  							<div class='card-body'>
-								<div class="tab-content" id="pills-tabContent">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %}
-  						  			<div class="tab-pane fade show active" id="{{amplicon_name}}_3a" role="tabpanel">
-							  			{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}}
-						  			</div>
-									{% endif %}
-
-									{% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %}
-  						  			<div class="tab-pane fade" id="{{amplicon_name}}_3b" role="tabpanel">
-							  			{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}}
-						  			</div>
-									{% endif %}
-  								</div>
-  							</div> {# end card_body #}
-  						</div> {# end card #}
-
-						<div class='card text-center mb-2'>
-  							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-  								<h5>Indel characterization</h5>
-								{% else %}
-  								<h5>Indel characterization for {{amplicon_name}}</h5>
-								{% endif %}
-  								<ul class="nav nav-tabs justify-content-center card-header-tabs" id="indel-characterization-tabs" role="tablist">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4a" role="tab" aria-controls="{{amplicon_name}}_4a" aria-selected="true">All Modifications Combined</button>
-  						  			</li>
-            								{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link active" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4b" role="tab" aria-controls="{{amplicon_name}}_4b" aria-selected="false">All Modifications by Type</button>
-  						  			</li>
-            								{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4c" role="tab" aria-controls="{{amplicon_name}}_4c" aria-selected="false">Modifications in Quantification Window</button>
-  						  			</li>
-            								{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4d" role="tab" aria-controls="{{amplicon_name}}_4d" aria-selected="false">Indel Lengths</button>
-  						  			</li>
-            								{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4e" role="tab" aria-controls="{{amplicon_name}}_4e" aria-selected="false">All reads aligned to {{amplicon_name}}</button>
-  						  			</li>
-								 	{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_4f" role="tab" aria-controls="{{amplicon_name}}_4f" aria-selected="false">HDR reads aligned to {{amplicon_name}}</button>
-  						  			</li>
-									{% endif %}
-  								</ul>
-  							</div> {# end card head #}
-  							<div class='card-body'>
-  								<div class="tab-content" id="pills-tabContent">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %}
-									<div class="tab-pane fade" id="{{amplicon_name}}_4a" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %}
-									<div class="tab-pane fade show active" id="{{amplicon_name}}_4b" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %}
-									<div class="tab-pane fade" id="{{amplicon_name}}_4c" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %}
-									<div class="tab-pane fade" id="{{amplicon_name}}_4d" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %}
-									<div class="tab-pane fade" id="{{amplicon_name}}_4e" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-
-									{% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %}
-									<div class="tab-pane fade" id="{{amplicon_name}}_4f" role="tabpanel">
-										{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}}
-									</div>
-									{% endif %}
-  								</div>
-  							</div> {# end card body #}
-  						</div> {# end card #}
-
-
-						{% if report_data['figures']['locs'][amplicon_name]['plot_5'] %}
-						<div class='card text-center mb-2'>
-							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Frameshift analysis</h5>
-								{% else %}
-  								<h5>Frameshift analysis for {{amplicon_name}}</h5>
-								{% endif %}
-							</div>
-  							<div class='card-body'>
-								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}}
-							</div>
-						</div>
-						{% endif %}
-
-						{% if report_data['figures']['locs'][amplicon_name]['plot_6'] %}
-						<div class='card text-center mb-2'>
-							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Frameshift mutagenesis profiles</h5>
-								{% else %}
-  								<h5>Frameshift mutagenesis profiles for {{amplicon_name}}</h5>
-								{% endif %}
-							</div>
-  							<div class='card-body'>
-								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}}
-							</div>
-						</div>
-						{% endif %}
-
-						{% if report_data['figures']['locs'][amplicon_name]['plot_7'] %}
-						<div class='card text-center mb-2'>
-							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Non-coding mutations</h5>
-								{% else %}
-  								<h5>Coding mutations for {{amplicon_name}}</h5>
-								{% endif %}
-							</div>
-  							<div class='card-body'>
-								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}}
-							</div>
-						</div>
-						{% endif %}
-
-						{% if report_data['figures']['locs'][amplicon_name]['plot_8'] %}
-						<div class='card text-center mb-2'>
-							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Splicing</h5>
-								{% else %}
-  								<h5>Splicing for {{amplicon_name}}</h5>
-								{% endif %}
-							</div>
-  							<div class='card-body'>
-								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}}
-							</div>
-						</div>
-						{% endif %}
-
-						{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and  report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%}
-						<div class='card text-center mb-2'>
-							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Allele plots</h5>
-								{% else %}
-  								<h5>Allele plots for {{amplicon_name}}</h5>
-								{% endif %}
-							</div>
-							<div class='card-body'>
-								{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %}
-                  				<div class='mb-4'>
-					  				{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}}
-                				</div>
-								{% endfor %}
-							</div>
-						</div>
-						{% endif %}
-
-						{% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %}
-  						<div class='card text-center mb-2'>
-  							<div class='card-header'>
-								{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
-								<h5>Base editing</h5>
-								{% else %}
-  								<h5>Base editing for {{amplicon_name}}</h5>
-								{% endif %}
-  								<ul class="nav nav-tabs justify-content-center card-header-tabs" id="aln-tab" role="tablist">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %}
-  						  			<li class="nav-item">
-						  				<button class="nav-link active" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_10a" role="tab" aria-controls="{{amplicon_name}}_10a" aria-selected="true">Substitution Frequencies</button>
-  						  			</li>
-									{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_10d" role="tab" aria-controls="{{amplicon_name}}_10d" aria-selected="false">Nucleotide Frequencies</button>
-  						  			</li>
-									{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_10e" role="tab" aria-controls="{{amplicon_name}}_10e" aria-selected="false">Base Proportions</button>
-  						  			</li>
-            						{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%}
-  						  			<li class="nav-item">
-						  				<button class="nav-link" data-bs-toggle="tab" data-bs-target="#{{amplicon_name}}_10f" role="tab" aria-controls="{{amplicon_name}}_10f" aria-selected="false">Non-reference Bases</button>
-  						  			</li>
-            						{% endif %}
-  								</ul>
-							</div>
-							<div class='card-body'>
-								<div class="tab-content" id="pills-tabContent">
-									{% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %}
-					  				<div class="tab-pane fade show active" id="{{amplicon_name}}_10a" role="tabpanel">
-                						<div class='mb-3'>
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}}
-                						</div>
-										<div>
-											<label class="labelpadding">Figures 10b,c: Substitution frequencies across the entire amplicon (left) and in the quantification window (right).</label>
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}}
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}}
-										</div>
-									</div>
-									{% else %}
-									<div class="tab-pane fade show active" id="{{amplicon_name}}_10a" role="tabpanel">
-										<div class='mb-3'>
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}}
-                						</div>
-                						<div>
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}}
-                						</div>
-  									</div>
-									{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%}
-									<div class="tab-pane fade" id="{{amplicon_name}}_10d" role="tabpanel">
-										{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %}
-										<div class='mb-4'>
-											{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}}
-										</div>
-										{% endfor %}
-									</div>
-									{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%}
-					  				<div class="tab-pane fade" id="{{amplicon_name}}_10e" role="tabpanel">
-						  				{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %}
-										<div class='mb-4'>
-			  								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}}
-  										</div>
-										{% endfor %}
-              						</div>
-									{% endif %}
-									{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%}
-									<div class="tab-pane fade" id="{{amplicon_name}}_10f" role="tabpanel">
-										{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %}
-                  						<div class='mb-4'>
-			  								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}}
-                  						</div>
-										{% endfor %}
-										{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %}
-                  						<div class='mb-4'>
-			  								{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}}
-                    					</div>
-										{% endfor %}
-									</div>
-								</div>
-							{% endif %}
-							</div>
-						</div> {# end card #}
-					{% endif %} {# end base editing card #}
-					</div> {# end this amplicon tab #} <!--end amp tab -->
-				{% endfor %}
-				</div> {# tab content #} <!-- end tab content -->
-			</div> <!-- end card -->
-		</div> {# jumbotron_content #} <!-- end jumbotron_content -->
-	</div> {# jumbrotron #} <!-- end jumbotron -->
-</div> {# column #} <!-- end column -->
-</center>
-
-<div class="col-sm-1"></div>
-{% endblock %}
-
-{% block foot %}
-<script>
-function updateZoom(e) {
-  /*prevent any other actions that may occur when moving over the image:*/
-//  e.preventDefault();
-  var img = e.target.imgObj
-  var view = e.target.viewObj
-  var lens = e.target.lensObj
-
-  if (!lens.hasWidthSet)
-  {
-    view_height = $('#'+view.id).height()
-    view_width = $('#'+view.id).width()
-    img_height = $('#'+img.id).height()
-    img_width = $('#'+img.id).width()
-    lens_height = $('#'+lens.id).height()
-    lens_width = $('#'+lens.id).width()
-
-    new_width = img_height * view_width/view_height  //make up for loss of precision
-    $('#'+lens.id).outerWidth(new_width)
-    lens.hasWidthSet = true
-
-    cx = view_width / new_width
-
-    view.view_height = view_height
-    view.view_width = view_width
-    img.img_height = img_height
-    img.img_width = img_width
-    lens.lens_height = lens_height
-    lens.lens_width = new_width
-
-  }
-
-  var pos, x, y;
-  /*get the cursor's x and y positions:*/
-  pos = getCursorPos(e,img);
-  /*calculate the position of the lens:*/
-  x = pos.x - (lens.lens_width / 2);
-  /*prevent the lens from being positioned outside the image:*/
-  if (x > img.img_width - lens.lens_width) {x = img.img_width - lens.lens_width;;
-  }
-  if (x < 0) {x = 0;}
-  lens.style.left = x + "px";
-  view.style.backgroundPosition = "-" + (x * cx) + "px 0px";
-}
-
-function getCursorPos(e,img) {
-  var a, x = 0, y = 0;
-  e = e || window.event;
-  /*get the x and y positions of the image:*/
-  a = img.getBoundingClientRect();
-  /*calculate the cursor's x and y coordinates, relative to the image:*/
-  x = e.pageX - a.left;
-  y = e.pageY - a.top;
-  /*consider any page scrolling:*/
-  x = x - window.pageXOffset;
-  y = y - window.pageYOffset;
-  return {x : x, y : y};
-}
-
-var passiveSupported = false;
-try {
-  var options = {
-    get passive() { // This function will be called when the browser
-                    //   attempts to access the passive property.
-      passiveSupported = true;
-    }
-  };
-
-  window.addEventListener("test", options, options);
-  window.removeEventListener("test", options, options);
-} catch(err) {
-  passiveSupported = false;
-}
-
-	{% for amplicon_name in report_data.amplicons %}
-		{% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %}
-		view = document.getElementById('zoomview_nucs_{{amplicon_name}}');
-		img = document.getElementById('tozoom_nucs_{{amplicon_name}}');
-		lens = document.getElementById('zoomlens_nucs_{{amplicon_name}}')
-
-		img.viewObj = view
-		img.lensObj = lens
-		img.imgObj = img
-
-		lens.viewObj = view
-		lens.lensObj = lens
-		lens.imgObj = img
-
-		lens.addEventListener("mousemove", updateZoom, passiveSupported? { passive: true } : false);
-		img.addEventListener("mousemove", updateZoom, passiveSupported? { passive: true } : false);
-		/*and also for touch screens:*/
-		lens.addEventListener("touchmove", updateZoom, passiveSupported? { passive: true } : false);
-		img.addEventListener("touchmove", updateZoom, passiveSupported? { passive: true } : false);
-
-		{% endif %}
-	{% endfor %}
-	</script>
-{% endblock %}
diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html
deleted file mode 100644
index 6f7e448e..00000000
--- a/templates/shared/partials/fig_reports.html
+++ /dev/null
@@ -1,31 +0,0 @@
-<div id="fig_{{fig_name}}">
-    {% if amplicon_name is defined %}
-        {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %}
-            {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}}
-        {% else %}
-        {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.png" width='40%' height='40%' ></a>
-            {% else %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.png" width='100%' height='100%' ></a>
-            {% endif %} 
-        {% endif %}
-        <label class="labelpadding">{{report_data['figures']['captions'][amplicon_name][fig_name]}}</label>
-        {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %}
-            <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-        {% endfor %}
-    {% else %}
-        {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %}
-            {{report_data['figures']['htmls'][fig_name]|safe}}
-        {% else %}
-            {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.png" width='40%' height='40%' ></a>
-            {% else %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.png" width='100%' height='100%' ></a>
-            {% endif %}        
-        {% endif %}
-        <label class="labelpadding">{{report_data['figures']['captions'][fig_name]}}</label>
-        {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %}
-            <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-        {% endfor %}
-    {% endif %}
-</div>
\ No newline at end of file
diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html
deleted file mode 100644
index e4e3297a..00000000
--- a/templates/shared/partials/fig_summaries.html
+++ /dev/null
@@ -1,11 +0,0 @@
-<div id="fig_summary_{{plot_name}}">
-    {% if report_data['htmls'][plot_name] %}
-        {{report_data['htmls'][plot_name]|safe}}
-    {% else %}
-        <a href="{{report_data['crispresso_data_path']}}{{plot_name}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{plot_name}}.png" width='70%'></a>
-    {% endif %}
-    <label class="labelpadding">{{report_data['labels'][plot_name]}}</label>
-    {% for (data_label,data_path) in report_data['datas'][plot_name] %}
-        <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
-    {% endfor %}
-</div>
diff --git a/templates/shared/partials/log_params.html b/templates/shared/partials/log_params.html
deleted file mode 100644
index ad035ae3..00000000
--- a/templates/shared/partials/log_params.html
+++ /dev/null
@@ -1,11 +0,0 @@
-<div class="tab-pane fade text-start" id="log_params" role="tabpanel">
-  <p>CRISPResso version: {{report_data['run_data']['running_info']['version']}}</p>
-  <p>Run completed: {{report_data['run_data']['running_info']['end_time_string']}}</p>
-  <p>Amplicon sequence: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args']['amplicon_seq']}}</pre></p>
-  {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %}
-  <p>Guide sequence: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args']['guide_seq']}}</pre></p>
-  {% endif %}
-  <p>Command used: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['command_used']}}</pre></p>
-  <p>Parameters: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args_string']}}</pre></p>
-  <p class='text-center m-0'><small><a href="{{report_data['crispresso_data_path']}}{{report_data['run_data']['running_info']['log_filename']}}">Running log</a></small></p>
-</div>
diff --git a/templates/wgsReport.html b/templates/wgsReport.html
deleted file mode 100644
index 0a5a1277..00000000
--- a/templates/wgsReport.html
+++ /dev/null
@@ -1,99 +0,0 @@
-{% extends "layout.html" %}
-{% block head %}
-<style>
-.nav-tabs.amp-header {
-  border-bottom:none !important;
-}
-
-.card-header.amp-header {
-  border-bottom:none !important;
-}
-.nav-tabs.amp-header .nav-link.active {
-  background-color:lightsteelblue;
-  border-bottom:lightsteelblue;
-}
-
-.tab-content.amp-body {
-  background-color:lightsteelblue;
-}
-
-@media print {
-   .tab-content > .tab-pane {
-    display: block !important;
-    opacity: 1 !important;
-    visibility: visible !important;
-		margin-bottom: 2em !important;
-		page-break-inside: avoid;
-  }
-  .nav-tabs {
-    display:none !important;
-    visibility:hidden !important;
-  }
-  .tab-content.amp-body {
-    background-color:transparent !important;
-  	border:None !important;
-  }
-}
-@media only screen and (max-width: 600px) {
-	.jumbotron img {
-		width:100%
-	}
-}
-</style>
-
-{% endblock %}
-
-{% block content %}
-<div class="row">
-<div class="col-sm-1"></div>
-<div class="col-sm-10">
-
-	<div class="jumbotron" style="background:rgba(0,0,0,0.0); padding:0px" >
-		<div id='jumbotron_content' >
-
-            <div class="card text-center mb-2">
-                <div class="card-header">
-                    <h5 id="{{report_name}}">{{report_name}}</h5>
-                </div>
-                <div class="card-body p-0">
-                    <div class="list-group list-group-flush">
-                        {% for region_name in run_names %}
-                        <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action" id="{{region_name}}">{{region_name}}</a>
-                        {% endfor %}
-                    </div>
-                </div>
-            </div>
-
-          {% if report_data['names']|length > 0 %}
-            {% for plot_name in report_data['names'] %}
-            <div class='card text-center mb-2'>
-              <div class='card-header'>
-                <h5>{{report_data['titles'][plot_name]}}</h5>
-              </div>
-              <div class='card-body' style='max-height:80vh;overflow-y:auto'>
-		        {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
-              </div>
-            </div>
-            {% endfor %}
-          {% endif %}
-
-           	<div align="center" class='p-3'>
-			     <a href="/reports_data/{{report_zip_filename}}" class="btn btn-primary" role="button"><i class="fas fa-download"></i> Download report</a>
-			     <a href="{{report_path}}" class="btn btn-primary" role="button"><i class="fas fa-link"></i> Link to report</a>
-                 <button class='btn btn-primary hidden-print' onclick='window.print();'><i class="fas fa-print"></i> Print</button>
-            </div>
-    {# data bit for web version: #}
-    {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
-    #}
-	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
-</div> {# jumbrotron #} <!-- end jumbotron -->
-
-</div> {# column #} <!-- end column -->
-
-<div class="col-sm-1"></div>
-</div>
-{% endblock %}
-
-{% block foot %}
-{% endblock %}