SYMBOL INDEX (662 symbols across 73 files)

FILE: docs/conf.py
  function setup (line 187) | def setup(app):

FILE: flowcraft/bin/merge_json.py
  function get_core_genes (line 14) | def get_core_genes(core_file):
  function filter_core_genes (line 23) | def filter_core_genes(locus_array, info_array, core_genes):
  function assess_quality (line 34) | def assess_quality(core_array, core_genes):
  function get_table_data (line 57) | def get_table_data(data_obj, sample_id=None):
  function main (line 83) | def main():

FILE: flowcraft/bin/parse_fasta.py
  function replace_char (line 9) | def replace_char(text):
  function getSequence (line 14) | def getSequence(ref, fasta):
  function main (line 32) | def main():

FILE: flowcraft/bin/parse_true_coverage.py
  function parse_true_coverage (line 7) | def parse_true_coverage(report_json, fail_json=None):
  function main (line 40) | def main():

FILE: flowcraft/bin/prepare_reports.py
  function write_json (line 12) | def write_json(report_json, version_json, trace_file, task_name,
  function main (line 63) | def main():

FILE: flowcraft/bin/renamePE_samtoolsFASTQ.py
  function formartFastqHeaders (line 34) | def formartFastqHeaders(in_fastq_1, in_fastq_2, outdir):
  function compressionType (line 79) | def compressionType(file_to_test):
  function runTime (line 93) | def runTime(start_time):
  function main (line 102) | def main():

FILE: flowcraft/flowcraft.py
  function get_args (line 41) | def get_args(args=None):
  function validate_build_arguments (line 196) | def validate_build_arguments(args):
  function copy_project (line 252) | def copy_project(path):
  function build (line 287) | def build(args):
  function inspect (line 381) | def inspect(args):
  function report (line 402) | def report(args):
  function main (line 423) | def main():

FILE: flowcraft/generator/components/alignment.py
  class Mafft (line 7) | class Mafft(Process):
    method __init__ (line 18) | def __init__(self, **kwargs):
  class ProgressiveMauve (line 45) | class ProgressiveMauve(Process):
    method __init__ (line 56) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/annotation.py
  class Abricate (line 8) | class Abricate(Process):
    method __init__ (line 23) | def __init__(self, **kwargs):
  class CardRgi (line 71) | class CardRgi(Process):
    method __init__ (line 81) | def __init__(self, **kwargs):
  class Prokka (line 109) | class Prokka(Process):
    method __init__ (line 124) | def __init__(self, **kwargs):
  class Diamond (line 163) | class Diamond(Process):
    method __init__ (line 173) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/assembly.py
  class Bcalm (line 8) | class Bcalm(Process):
    method __init__ (line 19) | def __init__(self, **kwargs):
  class Spades (line 51) | class Spades(Process):
    method __init__ (line 65) | def __init__(self, **kwargs):
  class Skesa (line 122) | class Skesa(Process):
    method __init__ (line 126) | def __init__(self, **kwargs):
  class ViralAssembly (line 153) | class ViralAssembly(Process):
    method __init__ (line 158) | def __init__(self, **kwargs):
  class Abyss (line 231) | class Abyss(Process):
    method __init__ (line 242) | def __init__(self, **kwargs):
  class Unicycler (line 267) | class Unicycler(Process):
    method __init__ (line 278) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/assembly_processing.py
  class ProcessSkesa (line 8) | class ProcessSkesa(Process):
    method __init__ (line 10) | def __init__(self, **kwargs):
  class ProcessSpades (line 54) | class ProcessSpades(Process):
    method __init__ (line 65) | def __init__(self, **kwargs):
  class AssemblyMapping (line 108) | class AssemblyMapping(Process):
    method __init__ (line 128) | def __init__(self, **kwargs):
  class Pilon (line 179) | class Pilon(Process):
    method __init__ (line 194) | def __init__(self, **kwargs):
  class Bandage (line 233) | class Bandage(Process):
    method __init__ (line 244) | def __init__(self, **kwargs):
  class Quast (line 266) | class Quast(Process):
    method __init__ (line 277) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/distance_estimation.py
  class MashDist (line 8) | class MashDist(Process):
    method __init__ (line 10) | def __init__(self, **kwargs):
  class MashScreen (line 69) | class MashScreen(Process):
    method __init__ (line 71) | def __init__(self, **kwargs):
  class MashSketchFasta (line 131) | class MashSketchFasta(Process):
    method __init__ (line 133) | def __init__(self, **kwargs):
  class MashSketchFastq (line 170) | class MashSketchFastq(MashSketchFasta):
    method __init__ (line 172) | def __init__(self, **kwargs):
  class FastAni (line 205) | class FastAni(Process):
    method __init__ (line 207) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/downloads.py
  class ReadsDownload (line 8) | class ReadsDownload(Process):
    method __init__ (line 18) | def __init__(self, **kwargs):
  class FasterqDump (line 44) | class FasterqDump(Process):
    method __init__ (line 54) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/mapping.py
  class Bowtie (line 7) | class Bowtie(Process):
    method __init__ (line 18) | def __init__(self, **kwargs):
  class RetrieveMapped (line 67) | class RetrieveMapped(Process):
    method __init__ (line 79) | def __init__(self, **kwargs):
  class Bwa (line 113) | class Bwa(Process):
    method __init__ (line 124) | def __init__(self, **kwargs):
  class MarkDuplicates (line 153) | class MarkDuplicates(Process):
    method __init__ (line 164) | def __init__(self, **kwargs):
  class BaseRecalibrator (line 186) | class BaseRecalibrator(Process):
    method __init__ (line 197) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/metagenomics.py
  class Concoct (line 8) | class Concoct(Process):
    method __init__ (line 24) | def __init__(self, **kwargs):
  class Kraken (line 76) | class Kraken(Process):
    method __init__ (line 85) | def __init__(self, **kwargs):
  class Kraken2 (line 113) | class Kraken2(Process):
    method __init__ (line 122) | def __init__(self, **kwargs):
  class Maxbin2 (line 151) | class Maxbin2(Process):
    method __init__ (line 167) | def __init__(self, **kwargs):
  class Megahit (line 216) | class Megahit(Process):
    method __init__ (line 230) | def __init__(self, **kwargs):
  class Metabat2 (line 284) | class Metabat2(Process):
    method __init__ (line 301) | def __init__(self, **kwargs):
  class Metaspades (line 344) | class Metaspades(Process):
    method __init__ (line 358) | def __init__(self, **kwargs):
  class Midas_species (line 396) | class Midas_species(Process):
    method __init__ (line 405) | def __init__(self, **kwargs):
  class RemoveHost (line 433) | class RemoveHost(Process):
    method __init__ (line 444) | def __init__(self, **kwargs):
  class Metaprob (line 482) | class Metaprob(Process):
    method __init__ (line 493) | def __init__(self, **kwargs):
  class SplitAssembly (line 526) | class SplitAssembly(Process):
    method __init__ (line 540) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/mlst.py
  class Mlst (line 7) | class Mlst(Process):
    method __init__ (line 22) | def __init__(self, **kwargs):
  class Chewbbaca (line 42) | class Chewbbaca(Process):
    method __init__ (line 57) | def __init__(self, **kwargs):
  class Metamlst (line 144) | class Metamlst(Process):
    method __init__ (line 155) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/patlas_mapping.py
  class MappingPatlas (line 7) | class MappingPatlas(Process):
    method __init__ (line 9) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/phylogeny.py
  class Raxml (line 7) | class Raxml(Process):
    method __init__ (line 18) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/reads_quality_control.py
  class IntegrityCoverage (line 8) | class IntegrityCoverage(Process):
    method __init__ (line 23) | def __init__(self, **kwargs):
  class CheckCoverage (line 49) | class CheckCoverage(Process):
    method __init__ (line 64) | def __init__(self, **kwargs):
  class TrueCoverage (line 90) | class TrueCoverage(Process):
    method __init__ (line 94) | def __init__(self, **kwargs):
  class Fastqc (line 120) | class Fastqc(Process):
    method __init__ (line 136) | def __init__(self, **kwargs):
  class Trimmomatic (line 164) | class Trimmomatic(Process):
    method __init__ (line 178) | def __init__(self, **kwargs):
  class FastqcTrimmomatic (line 237) | class FastqcTrimmomatic(Process):
    method __init__ (line 260) | def __init__(self, **kwargs):
  class FilterPoly (line 330) | class FilterPoly(Process):
    method __init__ (line 341) | def __init__(self, **kwargs):
  class DownsampleFastq (line 380) | class DownsampleFastq(Process):
    method __init__ (line 390) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/typing.py
  class SeqTyping (line 7) | class SeqTyping(Process):
    method __init__ (line 12) | def __init__(self, **kwargs):
  class PathoTyping (line 46) | class PathoTyping(Process):
    method __init__ (line 51) | def __init__(self, **kwargs):
  class Sistr (line 81) | class Sistr(Process):
    method __init__ (line 83) | def __init__(self, **kwargs):
  class Momps (line 98) | class Momps(Process):
    method __init__ (line 100) | def __init__(self, **kwargs):
  class DengueTyping (line 130) | class DengueTyping(Process):
    method __init__ (line 135) | def __init__(self, **kwargs):
  class Seroba (line 179) | class Seroba(Process):
    method __init__ (line 184) | def __init__(self, **kwargs):

FILE: flowcraft/generator/components/variant_calling.py
  class Haplotypecaller (line 7) | class Haplotypecaller(Process):
    method __init__ (line 18) | def __init__(self, **kwargs):

FILE: flowcraft/generator/engine.py
  class NextflowGenerator (line 33) | class NextflowGenerator:
    method __init__ (line 35) | def __init__(self, process_connections, nextflow_file, process_map,
    method _parse_process_name (line 184) | def _parse_process_name(name_str):
    method _build_connections (line 232) | def _build_connections(self, process_list, ignore_dependencies,
    method _get_process_names (line 374) | def _get_process_names(self, con, pid):
    method _add_dependency (line 408) | def _add_dependency(self, p, template, inlane, outlane, pid):
    method _search_tree_backwards (line 459) | def _search_tree_backwards(self, template, parent_lanes):
    method _test_connection (line 491) | def _test_connection(parent_process, child_process):
    method _build_header (line 518) | def _build_header(self):
    method _build_footer (line 527) | def _build_footer(self):
    method _update_raw_input (line 535) | def _update_raw_input(self, p, sink_channel=None, input_type=None):
    method _update_extra_inputs (line 580) | def _update_extra_inputs(self, p):
    method _get_fork_tree (line 636) | def _get_fork_tree(self, lane):
    method _set_implicit_link (line 660) | def _set_implicit_link(self, p, link):
    method _update_secondary_channels (line 691) | def _update_secondary_channels(self, p):
    method _set_channels (line 759) | def _set_channels(self):
    method _set_init_process (line 811) | def _set_init_process(self):
    method _set_secondary_channels (line 833) | def _set_secondary_channels(self):
    method _set_compiler_channels (line 865) | def _set_compiler_channels(self):
    method _set_general_compilers (line 872) | def _set_general_compilers(self):
    method _set_status_channels (line 904) | def _set_status_channels(self):
    method _get_resources_string (line 944) | def _get_resources_string(res_dict, pid):
    method _get_container_string (line 984) | def _get_container_string(cont_dict, pid):
    method _get_params_string (line 1028) | def _get_params_string(self):
    method _get_merged_params_string (line 1080) | def _get_merged_params_string(self):
    method _get_merged_params_string (line 1135) | def _get_merged_params_string(self):
    method _get_params_help (line 1176) | def _get_params_help(self):
    method _get_merged_params_help (line 1204) | def _get_merged_params_help(self):
    method _render_config (line 1238) | def _render_config(template, context):
    method _set_configurations (line 1249) | def _set_configurations(self):
    method dag_to_file (line 1303) | def dag_to_file(self, dict_viz, output_file=".treeDag.json"):
    method render_pipeline (line 1319) | def render_pipeline(self):
    method write_configs (line 1393) | def write_configs(self, project_root):
    method export_params (line 1430) | def export_params(self):
    method export_directives (line 1446) | def export_directives(self):
    method fetch_docker_tags (line 1459) | def fetch_docker_tags(self):
    method build (line 1570) | def build(self):

FILE: flowcraft/generator/error_handling.py
  class ProcessError (line 1) | class ProcessError(Exception):
    method __init__ (line 2) | def __init__(self, value):
    method __str__ (line 5) | def __str__(self):
  class SanityError (line 9) | class SanityError(Exception):
    method __init__ (line 13) | def __init__(self, value):
  class InspectionError (line 20) | class InspectionError(Exception):
    method __init__ (line 21) | def __init__(self, value):
  class ReportError (line 25) | class ReportError(Exception):
    method __init__ (line 26) | def __init__(self, value):
  class RecipeError (line 30) | class RecipeError(Exception):
    method __init__ (line 31) | def __init__(self, value):
  class LogError (line 37) | class LogError(Exception):
    method __init__ (line 38) | def __init__(self, value):

FILE: flowcraft/generator/inspect.py
  function signal_handler (line 35) | def signal_handler(screen):
  class NextflowInspector (line 53) | class NextflowInspector:
    method __init__ (line 61) | def __init__(self, trace_file, refresh_rate, pretty=False, ip_addr=None):
    method _check_required_files (line 267) | def _check_required_files(self):
    method _header_mapping (line 281) | def _header_mapping(header):
    method _expand_path (line 301) | def _expand_path(hash_str):
    method _hms (line 327) | def _hms(s):
    method _size_coverter (line 360) | def _size_coverter(s):
    method _size_compress (line 394) | def _size_compress(s):
    method _get_pipeline_processes (line 407) | def _get_pipeline_processes(self):
    method _clear_inspect (line 456) | def _clear_inspect(self):
    method _update_pipeline_status (line 477) | def _update_pipeline_status(self):
    method _update_tag_status (line 539) | def _update_tag_status(self, process, vals):
    method _update_barrier_status (line 601) | def _update_barrier_status(self):
    method _retrieve_log (line 623) | def _retrieve_log(path):
    method _update_trace_info (line 642) | def _update_trace_info(self, fields, hm):
    method _update_process_resources (line 715) | def _update_process_resources(self, process, vals):
    method _cpu_load_parser (line 729) | def _cpu_load_parser(self, cpus, cpu_per, t):
    method _assess_resource_warnings (line 753) | def _assess_resource_warnings(self, process, vals):
    method _update_process_stats (line 801) | def _update_process_stats(self):
    method trace_parser (line 893) | def trace_parser(self):
    method log_parser (line 937) | def log_parser(self):
    method update_inspection (line 1020) | def update_inspection(self):
    method display_overview (line 1049) | def display_overview(self):
    method _curses_keybindings (line 1089) | def _curses_keybindings(self):
    method _updown (line 1108) | def _updown(self, direction):
    method _rightleft (line 1119) | def _rightleft(self, direction):
    method flush_overview (line 1129) | def flush_overview(self):
    method _convert_process_dict (line 1248) | def _convert_process_dict(self):
    method _prepare_table_data (line 1263) | def _prepare_table_data(self):
    method _prepare_overview_data (line 1320) | def _prepare_overview_data(self):
    method _prepare_general_details (line 1336) | def _prepare_general_details(self):
    method _get_log_lines (line 1356) | def _get_log_lines(self, n=300):
    method _prepare_run_status_data (line 1375) | def _prepare_run_status_data(self):
    method _send_status_info (line 1388) | def _send_status_info(self, run_id):
    method _prepare_static_info (line 1432) | def _prepare_static_info(self):
    method _dag_file_to_dict (line 1467) | def _dag_file_to_dict(self):
    method _establish_connection (line 1488) | def _establish_connection(self, run_id, dict_dag):
    method _close_connection (line 1517) | def _close_connection(self, run_id):
    method _get_run_hash (line 1533) | def _get_run_hash(self):
    method _print_msg (line 1552) | def _print_msg(self, run_id):
    method broadcast_status (line 1560) | def broadcast_status(self):

FILE: flowcraft/generator/pipeline_parser.py
  function guess_process (line 24) | def guess_process(query_str, process_map):
  function remove_inner_forks (line 58) | def remove_inner_forks(text):
  function empty_tasks (line 87) | def empty_tasks(p_string):
  function brackets_but_no_lanes (line 103) | def brackets_but_no_lanes(p_string):
  function brackets_insanity_check (line 120) | def brackets_insanity_check(p_string):
  function lane_char_insanity_check (line 150) | def lane_char_insanity_check(p_string):
  function final_char_insanity_check (line 167) | def final_char_insanity_check(p_string):
  function fork_procs_insanity_check (line 186) | def fork_procs_insanity_check(p_string):
  function start_proc_insanity_check (line 213) | def start_proc_insanity_check(p_string):
  function late_proc_insanity_check (line 232) | def late_proc_insanity_check(p_string):
  function inner_fork_insanity_checks (line 250) | def inner_fork_insanity_checks(pipeline_string):
  function insanity_checks (line 305) | def insanity_checks(pipeline_str):
  function parse_pipeline (line 341) | def parse_pipeline(pipeline_str):
  function get_source_lane (line 450) | def get_source_lane(fork_process, pipeline_list):
  function get_lanes (line 486) | def get_lanes(lanes_str):
  function linear_connection (line 535) | def linear_connection(plist, lane):
  function fork_connection (line 578) | def fork_connection(source, sink, source_lane, lane):
  function linear_lane_connection (line 627) | def linear_lane_connection(lane_list, lane):
  function add_unique_identifiers (line 657) | def add_unique_identifiers(pipeline_str):
  function remove_unique_identifiers (line 730) | def remove_unique_identifiers(identifiers_to_tags, pipeline_links):

FILE: flowcraft/generator/process.py
  class Process (line 15) | class Process:
    method __init__ (line 105) | def __init__(self, template):
    method _set_template (line 308) | def _set_template(self, template):
    method set_main_channel_names (line 330) | def set_main_channel_names(self, input_suffix, output_suffix, lane):
    method set_param_id (line 350) | def set_param_id(self, param_id):
    method get_user_channel (line 362) | def get_user_channel(self, input_channel, input_type=None):
    method render (line 402) | def render(template, context):
    method template_str (line 420) | def template_str(self):
    method set_channels (line 444) | def set_channels(self, **kwargs):
    method update_main_input (line 489) | def update_main_input(self, input_str):
    method update_main_forks (line 494) | def update_main_forks(self, sink):
    method set_secondary_channel (line 518) | def set_secondary_channel(self, source, channel_list):
    method update_attributes (line 569) | def update_attributes(self, attr_dict):
  class Compiler (line 611) | class Compiler(Process):
    method __init__ (line 615) | def __init__(self, **kwargs):
    method set_compiler_channels (line 622) | def set_compiler_channels(self, channel_list, operator="mix"):
  class Init (line 676) | class Init(Process):
    method __init__ (line 678) | def __init__(self, **kwargs):
    method set_raw_inputs (line 687) | def set_raw_inputs(self, raw_input):
    method set_secondary_inputs (line 739) | def set_secondary_inputs(self, channel_dict):
    method set_extra_inputs (line 757) | def set_extra_inputs(self, channel_dict):
  class StatusCompiler (line 803) | class StatusCompiler(Compiler):
    method __init__ (line 810) | def __init__(self, **kwargs):
  class ReportCompiler (line 815) | class ReportCompiler(Compiler):
    method __init__ (line 822) | def __init__(self, **kwargs):
  class PatlasConsensus (line 827) | class PatlasConsensus(Compiler):
    method __init__ (line 834) | def __init__(self, **kwargs):

FILE: flowcraft/generator/process_collector.py
  function convert_camel_case (line 10) | def convert_camel_case(name):
  function collect_process_map (line 28) | def collect_process_map():

FILE: flowcraft/generator/process_details.py
  function colored_print (line 18) | def colored_print(msg, color_label="white_bold"):
  function procs_dict_parser (line 50) | def procs_dict_parser(procs_dict):
  function proc_collector (line 110) | def proc_collector(process_map, args, pipeline_string):

FILE: flowcraft/generator/recipe.py
  class InnuendoRecipe (line 19) | class InnuendoRecipe:
    method __init__ (line 21) | def __init__(self):
    method validate_pipeline (line 54) | def validate_pipeline(pipeline_string):
    method build_upstream (line 77) | def build_upstream(self, process_descriptions, task, all_tasks,
    method build_downstream (line 165) | def build_downstream(self, process_descriptions, task, all_tasks,
    method define_pipeline_string (line 237) | def define_pipeline_string(self, process_descriptions, tasks,
    method build_pipeline_string (line 350) | def build_pipeline_string(self, forks):
    method run_auto_pipeline (line 455) | def run_auto_pipeline(self, tasks):
  class Innuendo (line 491) | class Innuendo(InnuendoRecipe):
    method __init__ (line 497) | def __init__(self, *args, **kwargs):
  function brew_innuendo (line 528) | def brew_innuendo(args):
  class Recipe (line 564) | class Recipe:
    method __init__ (line 566) | def __init__(self):
    method brew (line 584) | def brew(self):
    method _get_component_str (line 614) | def _get_component_str(component, params=None, directives=None):
  function brew_recipe (line 649) | def brew_recipe(recipe_name):
  function list_recipes (line 691) | def list_recipes(full=False):

FILE: flowcraft/generator/recipes/denim.py
  class Denim (line 7) | class Denim(Recipe):
    method __init__ (line 13) | def __init__(self):

FILE: flowcraft/generator/recipes/innuca.py
  class Innuca (line 7) | class Innuca(Recipe):
    method __init__ (line 14) | def __init__(self):

FILE: flowcraft/generator/recipes/plasmids.py
  class Plasmids (line 7) | class Plasmids(Recipe):
    method __init__ (line 14) | def __init__(self):
  class PlasmidsMapping (line 33) | class PlasmidsMapping(Recipe):
    method __init__ (line 39) | def __init__(self):
  class PlasmidsAssembly (line 56) | class PlasmidsAssembly(Recipe):
    method __init__ (line 62) | def __init__(self):
  class PlasmidsMash (line 81) | class PlasmidsMash(Recipe):
    method __init__ (line 87) | def __init__(self):

FILE: flowcraft/generator/report.py
  function signal_handler (line 28) | def signal_handler():
  class FlowcraftReport (line 37) | class FlowcraftReport:
    method __init__ (line 39) | def __init__(self, report_file, trace_file=None, log_file=None,
    method _check_required_files (line 129) | def _check_required_files(self):
    method _header_mapping (line 136) | def _header_mapping(header):
    method _expand_path (line 156) | def _expand_path(hash_str):
    method _get_report_id (line 181) | def _get_report_id(self):
    method _update_pipeline_status (line 219) | def _update_pipeline_status(self):
    method update_trace_watch (line 247) | def update_trace_watch(self):
    method update_log_watch (line 293) | def update_log_watch(self):
    method _send_live_report (line 309) | def _send_live_report(self, report_id):
    method _init_live_reports (line 381) | def _init_live_reports(self, report_id):
    method _close_connection (line 416) | def _close_connection(self, report_id):
    method _send_report (line 443) | def _send_report(self, report_id):
    method _print_msg (line 464) | def _print_msg(self, run_id):
    method broadcast_report (line 473) | def broadcast_report(self):

FILE: flowcraft/generator/utils.py
  function get_nextflow_filepath (line 9) | def get_nextflow_filepath(log_file):

FILE: flowcraft/templates/assembly_report.py
  function __get_version_pilon (line 51) | def __get_version_pilon():
  class Assembly (line 84) | class Assembly:
    method __init__ (line 98) | def __init__(self, assembly_file, sample_id):
    method _parse_assembly (line 143) | def _parse_assembly(self, assembly_file):
    method _get_contig_id (line 184) | def _get_contig_id(contig_str):
    method get_summary_stats (line 213) | def get_summary_stats(self, output_csv=None):
    method _get_window_labels (line 284) | def _get_window_labels(self, window):
    method _gc_prop (line 318) | def _gc_prop(s, length):
    method get_gc_sliding (line 336) | def get_gc_sliding(self, window=2000):
    method _get_coverage_from_file (line 361) | def _get_coverage_from_file(self, coverage_file):
    method get_coverage_sliding (line 388) | def get_coverage_sliding(self, coverage_file, window=2000):
  function main (line 423) | def main(sample_id, assembly_file, coverage_bp_file=None):

FILE: flowcraft/templates/compile_reports.py
  function main (line 32) | def main(reports, forks, dag, main_js):

FILE: flowcraft/templates/dengue_typing_assembly.py
  function __get_version_seq_typing (line 56) | def __get_version_seq_typing():
  function replace_char (line 76) | def replace_char(text):
  function getSequence (line 90) | def getSequence(ref, fasta):
  function get_reference_header (line 122) | def get_reference_header(file):
  function getType (line 136) | def getType(file):
  function getScore (line 149) | def getScore(file):
  function main (line 178) | def main(sample_id, assembly, reference, result):

FILE: flowcraft/templates/dengue_typing_reads.py
  function __get_version_seq_typing (line 60) | def __get_version_seq_typing():
  function replace_char (line 81) | def replace_char(text):
  function getSequence (line 95) | def getSequence(ref, fasta):
  function get_reference_header (line 127) | def get_reference_header(file):
  function getType (line 141) | def getType(file):
  function getConsesusSequence (line 154) | def getConsesusSequence(best_reference, consensus, sample_id):
  function getScore (line 186) | def getScore(file):
  function main (line 219) | def main(sample_id, assembly, fastq_pair, reference, result):

FILE: flowcraft/templates/downsample_fastq.py
  function __get_version_spades (line 72) | def __get_version_spades():
  function main (line 99) | def main(sample_id, fastq_pair, genome_size, depth, clear, seed):

FILE: flowcraft/templates/fasta_spliter.py
  function main (line 19) | def main():

FILE: flowcraft/templates/fastqc.py
  function __get_version_fastqc (line 50) | def __get_version_fastqc():
  function convert_adatpers (line 81) | def convert_adatpers(adapter_fasta):
  function main (line 133) | def main(fastq_pair, adapter_file, cpus):

FILE: flowcraft/templates/fastqc_report.py
  function _get_quality_stats (line 78) | def _get_quality_stats(d, start_str, field_start=1, field_end=2):
  function write_json_report (line 131) | def write_json_report(sample_id, data1, data2):
  function get_trim_index (line 192) | def get_trim_index(biased_list):
  function trim_range (line 244) | def trim_range(data_file):
  function get_sample_trim (line 324) | def get_sample_trim(p1_data, p2_data):
  function get_summary (line 362) | def get_summary(summary_file):
  function check_summary_health (line 409) | def check_summary_health(summary_file, **kwargs):
  function main (line 521) | def main(sample_id, result_p1, result_p2, opts):

FILE: flowcraft/templates/flowcraft_utils/flowcraft_base.py
  function get_logger (line 14) | def get_logger(filepath, level=logging.DEBUG):
  function log_error (line 31) | def log_error():
  class MainWrapper (line 39) | class MainWrapper:
    method __init__ (line 41) | def __init__(self, f):
    method __call__ (line 47) | def __call__(self, *args, **kwargs):
    method build_versions (line 67) | def build_versions(self):

FILE: flowcraft/templates/integrity_coverage.py
  function guess_file_compression (line 140) | def guess_file_compression(file_path, magic_dict=None):
  function get_qual_range (line 183) | def get_qual_range(qual_str):
  function get_encodings_in_range (line 204) | def get_encodings_in_range(rmin, rmax):
  function main (line 241) | def main(sample_id, fastq_pair, gsize, minimum_coverage, opts):

FILE: flowcraft/templates/mapping2json.py
  function depth_file_reader (line 74) | def depth_file_reader(depth_file):
  function generate_jsons (line 115) | def generate_jsons(depth_dic_coverage, plasmid_length, cutoff):
  function main (line 195) | def main(depth_file, json_dict, cutoff, sample_id):

FILE: flowcraft/templates/mashdist2json.py
  function send_to_output (line 49) | def send_to_output(master_dict, mash_output, sample_id, assembly_file):
  function main (line 118) | def main(mash_output, hash_cutoff, sample_id, assembly_file):

FILE: flowcraft/templates/mashscreen2json.py
  function main (line 46) | def main(mash_output, sample_id):

FILE: flowcraft/templates/megahit.py
  function is_odd (line 55) | def is_odd(k_mer):
  function __get_version_megahit (line 62) | def __get_version_megahit():
  function set_kmers (line 98) | def set_kmers(kmer_opt, max_read_len):
  function fix_contig_names (line 149) | def fix_contig_names(asseembly_path):
  function clean_up (line 177) | def clean_up(fastq):
  function main (line 197) | def main(sample_id, fastq_pair, max_len, kmer, mem, clear):

FILE: flowcraft/templates/metaspades.py
  function __get_version_spades (line 53) | def __get_version_spades():
  function clean_up (line 88) | def clean_up(fastq):
  function set_kmers (line 107) | def set_kmers(kmer_opt, max_read_len):
  function main (line 154) | def main(sample_id, fastq_pair, max_len, kmer, clear):

FILE: flowcraft/templates/pATLAS_consensus_json.py
  function main (line 48) | def main(list_of_jsons):

FILE: flowcraft/templates/pipeline_status.py
  function get_json_info (line 45) | def get_json_info(fields, header):
  function get_previous_stats (line 62) | def get_previous_stats(stats_path):
  function main (line 88) | def main(sample_id, trace_file, workdir):

FILE: flowcraft/templates/process_abricate.py
  function __get_version_abricate (line 47) | def __get_version_abricate():
  class Abricate (line 90) | class Abricate:
    method __init__ (line 104) | def __init__(self, fls):
    method parse_files (line 131) | def parse_files(self, fls):
    method _parser (line 152) | def _parser(self, fl):
    method _test_truth (line 210) | def _test_truth(x, op, y):
    method iter_filter (line 242) | def iter_filter(self, filters, databases=None, fields=None,
    method get_filter (line 342) | def get_filter(self, *args, **kwargs):
  class AbricateReport (line 361) | class AbricateReport(Abricate):
    method __init__ (line 376) | def __init__(self, *args, **kwargs):
    method _get_contig_id (line 380) | def _get_contig_id(contig_str):
    method get_plot_data (line 409) | def get_plot_data(self):
    method get_table_data (line 476) | def get_table_data(self):
    method write_report_data (line 527) | def write_report_data(self):
  function main (line 543) | def main(abr_file):

FILE: flowcraft/templates/process_assembly.py
  class Assembly (line 75) | class Assembly:
    method __init__ (line 96) | def __init__(self, assembly_file, min_contig_len, min_kmer_cov,
    method _parse_coverage (line 141) | def _parse_coverage(header_str):
    method _parse_assembly (line 173) | def _parse_assembly(self, assembly_file):
    method _populate_contigs (line 241) | def _populate_contigs(self, contig_id, header, cov, sequence):
    method _get_gc_content (line 278) | def _get_gc_content(sequence, length):
    method _test_truth (line 309) | def _test_truth(x, op, y):
    method filter_contigs (line 341) | def filter_contigs(self, *comparisons):
    method get_assembly_length (line 390) | def get_assembly_length(self):
    method write_assembly (line 404) | def write_assembly(self, output_file, filtered=True):
    method write_report (line 428) | def write_report(self, output_file):
  function main (line 447) | def main(sample_id, assembly_file, gsize, opts, assembler):

FILE: flowcraft/templates/process_assembly_mapping.py
  function __get_version_samtools (line 67) | def __get_version_samtools():
  function __get_version_bowtie2 (line 85) | def __get_version_bowtie2():
  function parse_coverage_table (line 122) | def parse_coverage_table(coverage_file):
  function filter_assembly (line 167) | def filter_assembly(assembly_file, minimum_coverage, coverage_info,
  function filter_bam (line 212) | def filter_bam(coverage_info, bam_file, min_coverage, output_bam):
  function check_filtered_assembly (line 304) | def check_filtered_assembly(coverage_info, coverage_bp, minimum_coverage,
  function get_coverage_from_file (line 444) | def get_coverage_from_file(coverage_file):
  function evaluate_min_coverage (line 475) | def evaluate_min_coverage(coverage_opt, assembly_coverage, assembly_size):
  function get_assembly_size (line 518) | def get_assembly_size(assembly_file):
  function main (line 560) | def main(sample_id, assembly_file, coverage_file, coverage_bp_file, bam_...

FILE: flowcraft/templates/process_concoct.py
  function parse_assembly (line 43) | def parse_assembly(file):
  function parse_cluster_csv (line 62) | def parse_cluster_csv(file):
  function get_GC (line 82) | def get_GC(sequence):
  function merge_data (line 87) | def merge_data(contigs, clusters):
  function main (line 115) | def main(sample_id, cluster_file, contig_file):

FILE: flowcraft/templates/process_mapping.py
  class Bowtie (line 56) | class Bowtie:
    method __init__ (line 62) | def __init__(self, sample_id, bowtie_log):
    method set_n_reads (line 83) | def set_n_reads(self, n_reads):
    method set_align_0x (line 87) | def set_align_0x(self,align_0x):
    method set_align_1x (line 91) | def set_align_1x(self,align_1x):
    method set_align_mt1x (line 95) | def set_align_mt1x(self,align_mt1x):
    method set_overall_rate (line 99) | def set_overall_rate(self,overall_rate):
    method parse_log (line 103) | def parse_log(self, bowtie_log):
  function main (line 196) | def main(sample_id, bowite_log):

FILE: flowcraft/templates/process_metabat.py
  function parse_assembly (line 41) | def parse_assembly(file):
  function get_cg (line 60) | def get_cg(sequence):
  function get_bin_stats (line 65) | def get_bin_stats(bin_file):
  function main (line 78) | def main(sample_id, bins):

FILE: flowcraft/templates/process_newick.py
  function main (line 55) | def main(newick, labels):

FILE: flowcraft/templates/process_tsv.py
  function main (line 39) | def main(sample_id, tsv_file):

FILE: flowcraft/templates/process_viral_assembly.py
  class Assembly (line 58) | class Assembly:
    method __init__ (line 79) | def __init__(self, assembly_file, min_contig_len, min_kmer_cov,
    method getORFs (line 127) | def getORFs(self, assembly, min_size):
    method _parse_coverage (line 144) | def _parse_coverage(header_str):
    method _parse_assembly (line 176) | def _parse_assembly(self, assembly_file):
    method _populate_contigs (line 244) | def _populate_contigs(self, contig_id, header, cov, sequence):
    method _get_gc_content (line 281) | def _get_gc_content(sequence, length):
    method _test_truth (line 312) | def _test_truth(x, op, y):
    method filter_contigs (line 344) | def filter_contigs(self, *comparisons):
    method get_assembly_length (line 393) | def get_assembly_length(self):
    method write_assembly (line 407) | def write_assembly(self, output_file, filtered=True):
    method write_report (line 431) | def write_report(self, output_file):
  function main (line 451) | def main(sample_id, assembly_file, minsize):

FILE: flowcraft/templates/skesa.py
  function __get_version_skesa (line 50) | def __get_version_skesa():
  function clean_up (line 84) | def clean_up(fastq):
  function main (line 104) | def main(sample_id, fastq_pair, clear):

FILE: flowcraft/templates/spades.py
  function __get_version_spades (line 62) | def __get_version_spades():
  function set_kmers (line 102) | def set_kmers(kmer_opt, max_read_len):
  function clean_up (line 148) | def clean_up(fastq):
  function main (line 168) | def main(sample_id, fastq_pair, max_len, kmer, opts, clear, disable_rr):

FILE: flowcraft/templates/split_fasta.py
  function main (line 51) | def main(sample_id, assembly, min_size):

FILE: flowcraft/templates/trimmomatic.py
  function __get_version_trimmomatic (line 70) | def __get_version_trimmomatic():
  function parse_log (line 113) | def parse_log(log_file):
  function write_report (line 182) | def write_report(storage_dic, output_file, sample_id):
  function trimmomatic_log (line 226) | def trimmomatic_log(log_file, sample_id):
  function clean_up (line 242) | def clean_up(fastq_pairs, clear):
  function merge_default_adapters (line 265) | def merge_default_adapters():
  function main (line 287) | def main(sample_id, fastq_pair, trim_range, trim_opts, phred, adapters_f...

FILE: flowcraft/templates/trimmomatic_report.py
  function parse_log (line 48) | def parse_log(log_file):
  function write_report (line 117) | def write_report(storage_dic, output_file, sample_id):
  function main (line 164) | def main(log_files):

FILE: flowcraft/tests/test_assemblerflow.py
  function tmp (line 10) | def tmp():
  function test_check (line 17) | def test_check():
  function test_check_invalid (line 26) | def test_check_invalid():
  function test_build_file (line 35) | def test_build_file(tmp):
  function test_build_file_2 (line 45) | def test_build_file_2(tmp):
  function test_build_recipe (line 61) | def test_build_recipe(tmp):
  function test_build_recipe_innuendo (line 71) | def test_build_recipe_innuendo(tmp):

FILE: flowcraft/tests/test_broadcast.py
  function test_empty_log (line 8) | def test_empty_log():
  function test_no_path_in_log (line 14) | def test_no_path_in_log():
  function test_path_in_log (line 20) | def test_path_in_log():
  function test_regex_in_log (line 27) | def test_regex_in_log():

FILE: flowcraft/tests/test_engine.py
  function single_con (line 15) | def single_con():
  function single_status (line 27) | def single_status():
  function single_con_fasta (line 36) | def single_con_fasta():
  function single_con_multi_raw (line 45) | def single_con_multi_raw():
  function implicit_link (line 56) | def implicit_link():
  function implicit_link_2 (line 71) | def implicit_link_2():
  function single_fork (line 84) | def single_fork():
  function raw_forks (line 101) | def raw_forks():
  function multi_forks (line 116) | def multi_forks():
  function test_simple_init (line 141) | def test_simple_init():
  function test_invalid_process (line 156) | def test_invalid_process():
  function test_connections_single_process_channels (line 165) | def test_connections_single_process_channels(single_con):
  function test_connections_invalid (line 175) | def test_connections_invalid():
  function test_connections_ignore_type (line 187) | def test_connections_ignore_type():
  function test_build_header (line 198) | def test_build_header(single_con):
  function test_connections_nofork (line 205) | def test_connections_nofork(single_con):
  function test_connections_singlefork (line 210) | def test_connections_singlefork(single_fork):
  function test_connections_rawfork (line 215) | def test_connections_rawfork(raw_forks):
  function test_connections_multiforks (line 220) | def test_connections_multiforks(multi_forks):
  function test_connections_no_fork_channel_update (line 225) | def test_connections_no_fork_channel_update(single_con):
  function test_connections_fork_channel_update (line 232) | def test_connections_fork_channel_update(single_fork):
  function test_connections_channel_update (line 239) | def test_connections_channel_update(single_con):
  function test_connections_channel_update_wfork (line 247) | def test_connections_channel_update_wfork(single_fork):
  function test_connections_channel_update_wfork_2 (line 257) | def test_connections_channel_update_wfork_2(single_fork):
  function test_connections_channel_update_wfork_3 (line 265) | def test_connections_channel_update_wfork_3(single_fork):
  function test_set_channels_single_con_raw_fastq (line 274) | def test_set_channels_single_con_raw_fastq(single_con):
  function test_set_channels_single_con_raw_fasta (line 284) | def test_set_channels_single_con_raw_fasta(single_con_fasta):
  function test_set_channels_multi_raw_input (line 295) | def test_set_channels_multi_raw_input(single_con_multi_raw):
  function test_set_channels_secondary_channels_nolink (line 306) | def test_set_channels_secondary_channels_nolink(single_con):
  function test_set_channels_secondary_chanels_link (line 313) | def test_set_channels_secondary_chanels_link(multi_forks):
  function test_set_secondary_inputs_raw_forks (line 323) | def test_set_secondary_inputs_raw_forks(raw_forks):
  function test_set_secondary_inputs_multi_raw (line 336) | def test_set_secondary_inputs_multi_raw(single_con_multi_raw):
  function test_set_secondary_channels (line 346) | def test_set_secondary_channels(multi_forks):
  function test_set_secondary_channels_2 (line 362) | def test_set_secondary_channels_2(multi_forks):
  function test_set_implicit_link (line 374) | def test_set_implicit_link(implicit_link):
  function test_set_implicit_link (line 384) | def test_set_implicit_link(implicit_link_2):
  function test_set_status_channels_multi (line 394) | def test_set_status_channels_multi(single_con):
  function test_set_status_channels_single (line 407) | def test_set_status_channels_single(single_status):
  function test_set_compiler_channels (line 418) | def test_set_compiler_channels(single_status):
  function test_set_status_channels_no_status (line 430) | def test_set_status_channels_no_status(single_status):
  function test_set_status_channels_duplicate_status (line 442) | def test_set_status_channels_duplicate_status(single_status):
  function test_build (line 452) | def test_build(multi_forks):
  function test_resources_string (line 459) | def test_resources_string(single_con):
  function test_resources_string_2 (line 469) | def test_resources_string_2(single_con):
  function test_resources_string_3 (line 479) | def test_resources_string_3(single_con):
  function test_container_string (line 491) | def test_container_string(single_con):
  function test_container_string_2 (line 501) | def test_container_string_2(single_con):
  function test_extra_inputs_1 (line 513) | def test_extra_inputs_1():
  function test_extra_inputs_2 (line 525) | def test_extra_inputs_2():
  function test_extra_inputs_3 (line 540) | def test_extra_inputs_3():
  function test_extra_inputs_default (line 556) | def test_extra_inputs_default():
  function test_extra_inputs_invalid (line 575) | def test_extra_inputs_invalid():
  function test_extra_inputs_invalid_2 (line 588) | def test_extra_inputs_invalid_2():
  function test_run_time_directives (line 604) | def test_run_time_directives():
  function test_run_time_directives_full (line 616) | def test_run_time_directives_full():
  function test_run_time_directives_invalid (line 634) | def test_run_time_directives_invalid():
  function test_not_automatic_dependency (line 645) | def test_not_automatic_dependency():
  function test_automatic_dependency (line 655) | def test_automatic_dependency():
  function test_automatic_dependency_2 (line 665) | def test_automatic_dependency_2():
  function test_automatic_dependency_3 (line 675) | def test_automatic_dependency_3():
  function test_automatic_dependency_wfork (line 686) | def test_automatic_dependency_wfork():
  function test_automatic_dependency_wfork_2 (line 698) | def test_automatic_dependency_wfork_2():
  function test_automatic_dependency_wfork_3 (line 711) | def test_automatic_dependency_wfork_3():
  function test_automatic_dependency_wfork_4 (line 727) | def test_automatic_dependency_wfork_4():
  function test_automatic_dependency_multi (line 743) | def test_automatic_dependency_multi():
  function test_automatic_dependency_non_raw (line 756) | def test_automatic_dependency_non_raw():
  function test_patlas_compiler_channels (line 768) | def test_patlas_compiler_channels():
  function test_patlas_compiler_channels_2 (line 783) | def test_patlas_compiler_channels_2():
  function test_patlas_compiler_channels_empty (line 796) | def test_patlas_compiler_channels_empty():

FILE: flowcraft/tests/test_pipeline_parser.py
  function test_get_lanes (line 8) | def test_get_lanes():
  function test_linear_connection (line 29) | def test_linear_connection():
  function test_two_fork_connection (line 56) | def test_two_fork_connection():
  function test_two_fork_connection_mismatch_lane (line 87) | def test_two_fork_connection_mismatch_lane():
  function test_multi_fork_connection (line 119) | def test_multi_fork_connection():
  function test_linear_lane_connection (line 158) | def test_linear_lane_connection():
  function test_linear_multi_lane_connection (line 182) | def test_linear_multi_lane_connection():
  function test_get_source_lane (line 206) | def test_get_source_lane():
  function test_get_source_lane_2 (line 223) | def test_get_source_lane_2():
  function test_parse_pipeline (line 244) | def test_parse_pipeline():
  function test_parse_pipeline_file (line 251) | def test_parse_pipeline_file():
  function test_unique_id_len (line 264) | def test_unique_id_len():
  function test_remove_id (line 284) | def test_remove_id():

FILE: flowcraft/tests/test_process_details.py
  function test_color_print (line 12) | def test_color_print():
  function test_long_list (line 20) | def test_long_list():
  function test_short_list (line 30) | def test_short_list():

FILE: flowcraft/tests/test_processes.py
  function mock_process (line 17) | def mock_process():
  function process_wchannels (line 23) | def process_wchannels():
  function mock_status (line 34) | def mock_status():
  function mock_patlas_compiler (line 39) | def mock_patlas_compiler():
  function mock_init (line 45) | def mock_init():
  function test_process_init (line 50) | def test_process_init():
  function test_set_correct_template (line 59) | def test_set_correct_template(mock_process):
  function test_set_wrong_template (line 66) | def test_set_wrong_template(mock_process):
  function test_template_render_empty (line 72) | def test_template_render_empty(mock_process):
  function test_template_render (line 78) | def test_template_render(process_wchannels):
  function test_main_channel_setup (line 86) | def test_main_channel_setup(mock_process):
  function test_main_raw_channel_self (line 95) | def test_main_raw_channel_self(mock_process):
  function test_main_raw_channel_fastq (line 106) | def test_main_raw_channel_fastq(mock_process):
  function test_main_raw_channel_fasta (line 114) | def test_main_raw_channel_fasta(mock_process):
  function test_main_raw_channel_invalid (line 122) | def test_main_raw_channel_invalid(mock_process):
  function test_channels_setup (line 129) | def test_channels_setup(process_wchannels):
  function test_channels_setup_withforks (line 143) | def test_channels_setup_withforks(process_wchannels):
  function test_setup_one_raw_fork (line 159) | def test_setup_one_raw_fork(process_wchannels):
  function test_setup_multiple_raw_forks (line 174) | def test_setup_multiple_raw_forks(process_wchannels):
  function test_channels_setup_status (line 189) | def test_channels_setup_status(process_wchannels):
  function test_update_main_fork_noprevious (line 199) | def test_update_main_fork_noprevious(process_wchannels):
  function test_secondary_channels_multisink (line 213) | def test_secondary_channels_multisink(process_wchannels):
  function test_secondary_channels_singlesink (line 222) | def test_secondary_channels_singlesink(process_wchannels):
  function test_secondary_channels_duplicatesink (line 231) | def test_secondary_channels_duplicatesink(process_wchannels):
  function test_status_init (line 240) | def test_status_init(mock_status):
  function test_status_channel_setup_empty (line 245) | def test_status_channel_setup_empty(mock_status):
  function test_status_channel_single (line 251) | def test_status_channel_single(mock_status):
  function test_status_channel_two (line 258) | def test_status_channel_two(mock_status):
  function test_status_channel_multiple (line 265) | def test_status_channel_multiple(mock_status):
  function test_init_process (line 272) | def test_init_process(mock_init):
  function test_init_raw_inputs_single (line 277) | def test_init_raw_inputs_single(mock_init):
  function test_init_raw_inputs_multi_forks (line 287) | def test_init_raw_inputs_multi_forks(mock_init):
  function test_init_multi_raw_inputs (line 297) | def test_init_multi_raw_inputs(mock_init):
  function test_init_secondary_inputs (line 312) | def test_init_secondary_inputs(mock_init):
  function test_init_multi_secondary_inputs (line 321) | def test_init_multi_secondary_inputs(mock_init):
  function test_directive_update (line 331) | def test_directive_update():
  function test_directive_update2 (line 340) | def test_directive_update2():
  function test_directive_update3 (line 351) | def test_directive_update3():
  function test_directive_update4 (line 365) | def test_directive_update4():
  function test_join_compiler (line 379) | def test_join_compiler(mock_patlas_compiler):
  function test_join_compiler_one_channel (line 387) | def test_join_compiler_one_channel(mock_patlas_compiler):

FILE: flowcraft/tests/test_recipes.py
  function test_empty_recipe (line 11) | def test_empty_recipe():
  function test_empty_pipeline_str (line 19) | def test_empty_pipeline_str():
  function test_basic_recipe (line 29) | def test_basic_recipe():
  function test_recipe_wdirectives (line 41) | def test_recipe_wdirectives():
  function test_recipe_partial_directives (line 64) | def test_recipe_partial_directives():
  function test_recipe_partial_directives2 (line 83) | def test_recipe_partial_directives2():
  function test_component_str (line 102) | def test_component_str():
  function test_component_str2 (line 117) | def test_component_str2():
  function test_component_str3 (line 133) | def test_component_str3():
  function test_brew_recipe (line 153) | def test_brew_recipe():
  function test_bad_recipe_name (line 160) | def test_bad_recipe_name():
  function test_all_recipes (line 166) | def test_all_recipes():
  function test_innuendo_recipe (line 180) | def test_innuendo_recipe():
  function test_innuendo_partial_recipe (line 187) | def test_innuendo_partial_recipe():
  function test_list_recipes (line 194) | def test_list_recipes():
  function test_list_recipes_full (line 199) | def test_list_recipes_full():

FILE: flowcraft/tests/test_sanity.py
  function not_raises (line 13) | def not_raises(exception, msg):
  function test_empty_tasks (line 19) | def test_empty_tasks():
  function test_no_brackets_fail (line 30) | def test_no_brackets_fail():
  function test_number_of_forks_fail (line 41) | def test_number_of_forks_fail():
  function test_lane_char_fail (line 53) | def test_lane_char_fail():
  function test_final_char_fail (line 64) | def test_final_char_fail():
  function test_fork_no_proc_fail (line 76) | def test_fork_no_proc_fail():
  function test_double_fork_fail (line 88) | def test_double_fork_fail():
  function test_close_token_ending_fail (line 99) | def test_close_token_ending_fail():
  function test_inner_forks_fail (line 110) | def test_inner_forks_fail():
  function test_string_pass_all (line 121) | def test_string_pass_all():
  function test_string_spaces_pass_all (line 143) | def test_string_spaces_pass_all():
  function test_string_pass_all_wrapper (line 161) | def test_string_pass_all_wrapper():