How to use multiqc - 10 common examples

def test_quality_control():
        report.files = {"sequana/quality_control":
            [ { 'fn': sequana_data('summary_qc.json'), 'root': '.'}]
        }
        quality_control.MultiqcModule()

def clean_s_name(self, s_name, root):
        """ Helper function to take a long file name and strip it
        back to a clean sample name. Somewhat arbitrary.
        :param s_name: The sample name to clean
        :param root: The directory path that this file is within
        :param prepend_dirs: boolean, whether to prepend dir name to s_name
        :param trimmed: boolean, remove common trimming suffixes from name?
        :return: The cleaned sample name, ready to be used
        """
        if root is None:
            root = ''
        # Split then take first section to remove everything after these matches
        for ext in config.fn_clean_exts:
            s_name = s_name.split(ext ,1)[0]
        if config.prepend_dirs:
            s_name = "{} | {}".format(root.replace(os.sep, ' | '), s_name).lstrip('. | ')
        return s_name

contigs_line.startswith("contigs:"),
                   bases_line.startswith("bases:"))):
            return

        # Get organism and sample name from the first line
        # Assumes organism name only consists of two words,
        # i.e. 'Genusname speciesname', and that the remaining
        # text on the organism line is the sample name.
        try:
            organism = " ".join(first_line.strip().split(":", 1)[1].split()[:2])
            s_name = self.clean_s_name(" ".join(first_line.split()[3:]), f['root'])
        except KeyError:
            organism = first_line.strip().split(":", 1)[1]
            s_name = f['s_name']
        # Don't try to guess sample name if requested in the config
        if getattr(config, 'prokka_fn_snames', False):
            s_name = f['s_name']

        if s_name in self.prokka:
            log.debug("Duplicate sample name found! Overwriting: {}".format(s_name))
        self.prokka[s_name] = dict()
        self.prokka[s_name]['organism'] = organism
        self.prokka[s_name]['contigs'] = int(contigs_line.split(":")[1])
        self.prokka[s_name]['bases'] = int(bases_line.split(":")[1])

        # Get additional info from remaining lines
        for line in f['f']:
            description, value = line.split(":")
            try:
                self.prokka[s_name][description] = int(value)
            except ValueError:
                log.warning("Unable to parse line: '%s'", line)

config.skip_generalstats = True
            config.exclude_modules = tuple(x for x in config.exclude_modules if x != 'general_stats')
        run_modules = [m for m in run_modules if list(m.keys())[0] not in config.exclude_modules]
    if len(run_modules) == 0:
        logger.critical('No analysis modules specified!')
        sys.exit(1)
    run_module_names = [ list(m.keys())[0] for m in run_modules ]
    logger.debug("Analysing modules: {}".format(', '.join(run_module_names)))

    # Create the temporary working directories
    tmp_dir = tempfile.mkdtemp()
    logger.debug('Using temporary directory for creating report: {}'.format(tmp_dir))
    config.data_tmp_dir = os.path.join(tmp_dir, 'multiqc_data')
    if filename != 'stdout' and config.make_data_dir == True:
        config.data_dir = config.data_tmp_dir
        os.makedirs(config.data_dir)
    else:
        config.data_dir = None
    config.plots_tmp_dir = os.path.join(tmp_dir, 'multiqc_plots')
    if filename != 'stdout' and config.export_plots == True:
        config.plots_dir = config.plots_tmp_dir
        os.makedirs(config.plots_dir)

    # Load the template
    template_mod = config.avail_templates[config.template].load()

    # Add an output subdirectory if specified by template
    try:
        config.output_dir = os.path.join(config.output_dir, template_mod.output_subdir)
    except AttributeError:
        pass # No subdirectory variable given

if not os.path.exists(os.path.dirname(config.output_fn)):
            os.makedirs(os.path.dirname(config.output_fn))
        logger.info("Report      : {}".format(os.path.relpath(config.output_fn)))

        if config.make_data_dir == False:
            logger.info("Data        : None")
        else:
            # Make directories for data_dir
            logger.info("Data        : {}".format(os.path.relpath(config.data_dir)))
            if not os.path.exists(config.data_dir):
                os.makedirs(config.data_dir)
            # Modules have run, so data directory should be complete by now. Move its contents.
            for f in os.listdir(config.data_tmp_dir):
                fn = os.path.join(config.data_tmp_dir, f)
                logger.debug("Moving data file from '{}' to '{}'".format(fn, config.data_dir))
                shutil.move(fn, config.data_dir)

        # Copy across the static plot images if requested
        if config.export_plots:
            config.plots_dir = os.path.join(config.output_dir, config.plots_dir_name)
            if os.path.exists(config.plots_dir):
                if config.force:
                    logger.warning("Deleting    : {}   (-f was specified)".format(os.path.relpath(config.plots_dir)))
                    shutil.rmtree(config.plots_dir)
                else:
                    logger.error("Output directory {} already exists.".format(config.plots_dir))
                    logger.info("Use -f or --force to overwrite existing reports")
                    shutil.rmtree(tmp_dir)
                    sys.exit(1)
            os.makedirs(config.plots_dir)
            logger.info("Plots       : {}".format(os.path.relpath(config.plots_dir)))

run_modules = [m for m in run_modules if list(m.keys())[0] not in config.exclude_modules]
    if len(run_modules) == 0:
        logger.critical('No analysis modules specified!')
        sys.exit(1)
    run_module_names = [ list(m.keys())[0] for m in run_modules ]
    logger.debug("Analysing modules: {}".format(', '.join(run_module_names)))

    # Create the temporary working directories
    tmp_dir = tempfile.mkdtemp()
    logger.debug('Using temporary directory for creating report: {}'.format(tmp_dir))
    config.data_tmp_dir = os.path.join(tmp_dir, 'multiqc_data')
    if filename != 'stdout' and config.make_data_dir == True:
        config.data_dir = config.data_tmp_dir
        os.makedirs(config.data_dir)
    else:
        config.data_dir = None
    config.plots_tmp_dir = os.path.join(tmp_dir, 'multiqc_plots')
    if filename != 'stdout' and config.export_plots == True:
        config.plots_dir = config.plots_tmp_dir
        os.makedirs(config.plots_dir)

    # Load the template
    template_mod = config.avail_templates[config.template].load()

    # Add an output subdirectory if specified by template
    try:
        config.output_dir = os.path.join(config.output_dir, template_mod.output_subdir)
    except AttributeError:
        pass # No subdirectory variable given


    # Add custom content section names

# Make directories for report if needed
        if not os.path.exists(os.path.dirname(config.output_fn)):
            os.makedirs(os.path.dirname(config.output_fn))
        logger.info("Report      : {}".format(os.path.relpath(config.output_fn)))

        if config.make_data_dir == False:
            logger.info("Data        : None")
        else:
            # Make directories for data_dir
            logger.info("Data        : {}".format(os.path.relpath(config.data_dir)))
            if not os.path.exists(config.data_dir):
                os.makedirs(config.data_dir)
            # Modules have run, so data directory should be complete by now. Move its contents.
            for f in os.listdir(config.data_tmp_dir):
                fn = os.path.join(config.data_tmp_dir, f)
                logger.debug("Moving data file from '{}' to '{}'".format(fn, config.data_dir))
                shutil.move(fn, config.data_dir)

        # Copy across the static plot images if requested
        if config.export_plots:
            config.plots_dir = os.path.join(config.output_dir, config.plots_dir_name)
            if os.path.exists(config.plots_dir):
                if config.force:
                    logger.warning("Deleting    : {}   (-f was specified)".format(os.path.relpath(config.plots_dir)))
                    shutil.rmtree(config.plots_dir)
                else:
                    logger.error("Output directory {} already exists.".format(config.plots_dir))
                    logger.info("Use -f or --force to overwrite existing reports")
                    shutil.rmtree(tmp_dir)
                    sys.exit(1)
            os.makedirs(config.plots_dir)
            logger.info("Plots       : {}".format(os.path.relpath(config.plots_dir)))

if config.make_data_dir == False:
            logger.info("Data        : None")
        else:
            # Make directories for data_dir
            logger.info("Data        : {}".format(os.path.relpath(config.data_dir)))
            if not os.path.exists(config.data_dir):
                os.makedirs(config.data_dir)
            # Modules have run, so data directory should be complete by now. Move its contents.
            for f in os.listdir(config.data_tmp_dir):
                fn = os.path.join(config.data_tmp_dir, f)
                logger.debug("Moving data file from '{}' to '{}'".format(fn, config.data_dir))
                shutil.move(fn, config.data_dir)

        # Copy across the static plot images if requested
        if config.export_plots:
            config.plots_dir = os.path.join(config.output_dir, config.plots_dir_name)
            if os.path.exists(config.plots_dir):
                if config.force:
                    logger.warning("Deleting    : {}   (-f was specified)".format(os.path.relpath(config.plots_dir)))
                    shutil.rmtree(config.plots_dir)
                else:
                    logger.error("Output directory {} already exists.".format(config.plots_dir))
                    logger.info("Use -f or --force to overwrite existing reports")
                    shutil.rmtree(tmp_dir)
                    sys.exit(1)
            os.makedirs(config.plots_dir)
            logger.info("Plots       : {}".format(os.path.relpath(config.plots_dir)))

            # Modules have run, so plots directory should be complete by now. Move its contents.
            for f in os.listdir(config.plots_tmp_dir):
                fn = os.path.join(config.plots_tmp_dir, f)
                logger.debug("Moving plots directory from '{}' to '{}'".format(fn, config.plots_dir))

shutil.move(fn, config.data_dir)

        # Copy across the static plot images if requested
        if config.export_plots:
            config.plots_dir = os.path.join(config.output_dir, config.plots_dir_name)
            if os.path.exists(config.plots_dir):
                if config.force:
                    logger.warning("Deleting    : {}   (-f was specified)".format(os.path.relpath(config.plots_dir)))
                    shutil.rmtree(config.plots_dir)
                else:
                    logger.error("Output directory {} already exists.".format(config.plots_dir))
                    logger.info("Use -f or --force to overwrite existing reports")
                    shutil.rmtree(tmp_dir)
                    sys.exit(1)
            os.makedirs(config.plots_dir)
            logger.info("Plots       : {}".format(os.path.relpath(config.plots_dir)))

            # Modules have run, so plots directory should be complete by now. Move its contents.
            for f in os.listdir(config.plots_tmp_dir):
                fn = os.path.join(config.plots_tmp_dir, f)
                logger.debug("Moving plots directory from '{}' to '{}'".format(fn, config.plots_dir))
                shutil.move(fn, config.plots_dir)

    plugin_hooks.mqc_trigger('before_template')

    # Load in parent template files first if a child theme
    try:
        parent_template = config.avail_templates[template_mod.template_parent].load()
        copy_tree(parent_template.template_dir, tmp_dir)
    except AttributeError:
        pass # Not a child theme

logger.info("Data        : None")
        else:
            # Make directories for data_dir
            logger.info("Data        : {}".format(os.path.relpath(config.data_dir)))
            if not os.path.exists(config.data_dir):
                os.makedirs(config.data_dir)
            # Modules have run, so data directory should be complete by now. Move its contents.
            for f in os.listdir(config.data_tmp_dir):
                fn = os.path.join(config.data_tmp_dir, f)
                logger.debug("Moving data file from '{}' to '{}'".format(fn, config.data_dir))
                shutil.move(fn, config.data_dir)

        # Copy across the static plot images if requested
        if config.export_plots:
            config.plots_dir = os.path.join(config.output_dir, config.plots_dir_name)
            if os.path.exists(config.plots_dir):
                if config.force:
                    logger.warning("Deleting    : {}   (-f was specified)".format(os.path.relpath(config.plots_dir)))
                    shutil.rmtree(config.plots_dir)
                else:
                    logger.error("Output directory {} already exists.".format(config.plots_dir))
                    logger.info("Use -f or --force to overwrite existing reports")
                    shutil.rmtree(tmp_dir)
                    sys.exit(1)
            os.makedirs(config.plots_dir)
            logger.info("Plots       : {}".format(os.path.relpath(config.plots_dir)))

            # Modules have run, so plots directory should be complete by now. Move its contents.
            for f in os.listdir(config.plots_tmp_dir):
                fn = os.path.join(config.plots_tmp_dir, f)
                logger.debug("Moving plots directory from '{}' to '{}'".format(fn, config.plots_dir))
                shutil.move(fn, config.plots_dir)