FlowCraft
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Recipe creation guidelines
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Source API
flowcraft package
FlowCraft
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Index
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C
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D
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E
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F
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I
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K
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Q
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W
A
Abricate (class in flowcraft.generator.components.annotation)
(class in flowcraft.templates.process_abricate)
AbricateReport (class in flowcraft.templates.process_abricate)
Abyss (class in flowcraft.generator.components.assembly)
add_unique_identifiers() (in module flowcraft.generator.pipeline_parser)
Assembly (class in flowcraft.templates.assembly_report)
(class in flowcraft.templates.process_assembly)
AssemblyMapping (class in flowcraft.generator.components.assembly_processing)
B
Bandage (class in flowcraft.generator.components.assembly_processing)
Bcalm (class in flowcraft.generator.components.assembly)
brackets_but_no_lanes() (in module flowcraft.generator.pipeline_parser)
brackets_insanity_check() (in module flowcraft.generator.pipeline_parser)
brew() (flowcraft.generator.recipe.Recipe method)
brew_innuendo() (in module flowcraft.generator.recipe)
brew_recipe() (in module flowcraft.generator.recipe)
build() (flowcraft.generator.engine.NextflowGenerator method)
build_downstream() (flowcraft.generator.recipe.InnuendoRecipe method)
build_pipeline_string() (flowcraft.generator.recipe.InnuendoRecipe method)
build_upstream() (flowcraft.generator.recipe.InnuendoRecipe method)
build_versions() (flowcraft.templates.flowcraft_utils.flowcraft_base.MainWrapper method)
C
CardRgi (class in flowcraft.generator.components.annotation)
check_filtered_assembly() (in module flowcraft.templates.process_assembly_mapping)
check_summary_health() (in module flowcraft.templates.fastqc_report)
CheckCoverage (class in flowcraft.generator.components.reads_quality_control)
Chewbbaca (class in flowcraft.generator.components.mlst)
clean_up() (in module flowcraft.templates.megahit)
(in module flowcraft.templates.metaspades)
(in module flowcraft.templates.skesa)
(in module flowcraft.templates.spades)
(in module flowcraft.templates.trimmomatic)
colored_print() (in module flowcraft.generator.process_details)
Compiler (class in flowcraft.generator.process)
compiler (flowcraft.generator.process.Process attribute)
compilers (flowcraft.generator.engine.NextflowGenerator attribute)
Concoct (class in flowcraft.generator.components.metagenomics)
config (flowcraft.generator.engine.NextflowGenerator attribute)
containers (flowcraft.generator.engine.NextflowGenerator attribute)
contig_boundaries (flowcraft.templates.assembly_report.Assembly attribute)
contig_coverage (flowcraft.templates.assembly_report.Assembly attribute)
contigs (flowcraft.templates.assembly_report.Assembly attribute)
(flowcraft.templates.process_assembly.Assembly attribute)
convert_adatpers() (in module flowcraft.templates.fastqc)
count_forks (flowcraft.generator.recipe.InnuendoRecipe attribute)
D
dag_to_file() (flowcraft.generator.engine.NextflowGenerator method)
define_pipeline_string() (flowcraft.generator.recipe.InnuendoRecipe method)
DengueTyping (class in flowcraft.generator.components.typing)
dependencies (flowcraft.generator.process.Process attribute)
Diamond (class in flowcraft.generator.components.annotation)
directives (flowcraft.generator.process.Process attribute)
(flowcraft.generator.recipe.Recipe attribute)
DownsampleFastq (class in flowcraft.generator.components.reads_quality_control)
E
empty_tasks() (in module flowcraft.generator.pipeline_parser)
evaluate_min_coverage() (in module flowcraft.templates.process_assembly_mapping)
export_directives() (flowcraft.generator.engine.NextflowGenerator method)
export_parameters (flowcraft.generator.engine.NextflowGenerator attribute)
export_params() (flowcraft.generator.engine.NextflowGenerator method)
extra_input (flowcraft.generator.process.Process attribute)
extra_inputs (flowcraft.generator.engine.NextflowGenerator attribute)
F
FastAni (class in flowcraft.generator.components.distance_estimation)
FasterqDump (class in flowcraft.generator.components.downloads)
Fastqc (class in flowcraft.generator.components.reads_quality_control)
FastqcTrimmomatic (class in flowcraft.generator.components.reads_quality_control)
fetch_docker_tags() (flowcraft.generator.engine.NextflowGenerator method)
filter_assembly() (in module flowcraft.templates.process_assembly_mapping)
filter_bam() (in module flowcraft.templates.process_assembly_mapping)
filter_contigs() (flowcraft.templates.process_assembly.Assembly method)
filtered_ids (flowcraft.templates.process_assembly.Assembly attribute)
FilterPoly (class in flowcraft.generator.components.reads_quality_control)
filters (flowcraft.templates.process_assembly.Assembly attribute)
final_char_insanity_check() (in module flowcraft.generator.pipeline_parser)
fix_contig_names() (in module flowcraft.templates.megahit)
flowcraft (module)
flowcraft.generator (module)
flowcraft.generator.components (module)
flowcraft.generator.components.annotation (module)
flowcraft.generator.components.assembly (module)
flowcraft.generator.components.assembly_processing (module)
flowcraft.generator.components.distance_estimation (module)
flowcraft.generator.components.downloads (module)
flowcraft.generator.components.metagenomics (module)
flowcraft.generator.components.mlst (module)
flowcraft.generator.components.patlas_mapping (module)
flowcraft.generator.components.reads_quality_control (module)
flowcraft.generator.components.typing (module)
flowcraft.generator.engine (module)
flowcraft.generator.error_handling (module)
flowcraft.generator.footer_skeleton (module)
flowcraft.generator.header_skeleton (module)
flowcraft.generator.pipeline_parser (module)
flowcraft.generator.process (module)
flowcraft.generator.process_details (module)
flowcraft.generator.recipe (module)
flowcraft.templates (module)
flowcraft.templates.assembly_report (module)
flowcraft.templates.fastqc (module)
flowcraft.templates.fastqc_report (module)
flowcraft.templates.flowcraft_utils (module)
flowcraft.templates.flowcraft_utils.flowcraft_base (module)
flowcraft.templates.integrity_coverage (module)
flowcraft.templates.mashdist2json (module)
flowcraft.templates.mashscreen2json (module)
flowcraft.templates.megahit (module)
flowcraft.templates.metaspades (module)
flowcraft.templates.pATLAS_consensus_json (module)
flowcraft.templates.pipeline_status (module)
flowcraft.templates.process_abricate (module)
flowcraft.templates.process_assembly (module)
flowcraft.templates.process_assembly_mapping (module)
flowcraft.templates.skesa (module)
flowcraft.templates.spades (module)
flowcraft.templates.trimmomatic (module)
flowcraft.templates.trimmomatic_report (module)
flowcraft.tests (module)
flowcraft.tests.data_pipelines (module)
flowcraft.tests.test_pipeline_parser (module)
fork_connection() (in module flowcraft.generator.pipeline_parser)
fork_procs_insanity_check() (in module flowcraft.generator.pipeline_parser)
forks (flowcraft.generator.process.Process attribute)
(flowcraft.generator.recipe.InnuendoRecipe attribute)
G
get_assembly_length() (flowcraft.templates.process_assembly.Assembly method)
get_assembly_size() (in module flowcraft.templates.process_assembly_mapping)
get_coverage_from_file() (in module flowcraft.templates.process_assembly_mapping)
get_coverage_sliding() (flowcraft.templates.assembly_report.Assembly method)
get_encodings_in_range() (in module flowcraft.templates.integrity_coverage)
get_filter() (flowcraft.templates.process_abricate.Abricate method)
get_gc_sliding() (flowcraft.templates.assembly_report.Assembly method)
get_json_info() (in module flowcraft.templates.pipeline_status)
get_lanes() (in module flowcraft.generator.pipeline_parser)
get_logger() (in module flowcraft.templates.flowcraft_utils.flowcraft_base)
get_plot_data() (flowcraft.templates.process_abricate.AbricateReport method)
get_previous_stats() (in module flowcraft.templates.pipeline_status)
get_qual_range() (in module flowcraft.templates.integrity_coverage)
get_sample_trim() (in module flowcraft.templates.fastqc_report)
get_source_lane() (in module flowcraft.generator.pipeline_parser)
get_summary() (in module flowcraft.templates.fastqc_report)
get_summary_stats() (flowcraft.templates.assembly_report.Assembly method)
get_table_data() (flowcraft.templates.process_abricate.AbricateReport method)
get_trim_index() (in module flowcraft.templates.fastqc_report)
get_user_channel() (flowcraft.generator.process.Process method)
guess_file_compression() (in module flowcraft.templates.integrity_coverage)
guess_process() (in module flowcraft.generator.pipeline_parser)
I
ignore_pid (flowcraft.generator.process.Process attribute)
ignore_type (flowcraft.generator.process.Process attribute)
Init (class in flowcraft.generator.process)
inner_fork_insanity_checks() (in module flowcraft.generator.pipeline_parser)
Innuendo (class in flowcraft.generator.recipe)
InnuendoRecipe (class in flowcraft.generator.recipe)
input_channel (flowcraft.generator.process.Process attribute)
input_type (flowcraft.generator.process.Process attribute)
input_user_channel (flowcraft.generator.process.Process attribute)
insanity_checks() (in module flowcraft.generator.pipeline_parser)
InspectionError
IntegrityCoverage (class in flowcraft.generator.components.reads_quality_control)
is_odd() (in module flowcraft.templates.megahit)
iter_filter() (flowcraft.templates.process_abricate.Abricate method)
K
Kraken (class in flowcraft.generator.components.metagenomics)
Kraken2 (class in flowcraft.generator.components.metagenomics)
L
lane_char_insanity_check() (in module flowcraft.generator.pipeline_parser)
lanes (flowcraft.generator.engine.NextflowGenerator attribute)
late_proc_insanity_check() (in module flowcraft.generator.pipeline_parser)
linear_connection() (in module flowcraft.generator.pipeline_parser)
linear_lane_connection() (in module flowcraft.generator.pipeline_parser)
link_end (flowcraft.generator.process.Process attribute)
link_start (flowcraft.generator.process.Process attribute)
list_recipes() (in module flowcraft.generator.recipe)
log_error() (in module flowcraft.templates.flowcraft_utils.flowcraft_base)
LogError
M
MAGIC_DICT (in module flowcraft.templates.integrity_coverage)
main_forks (flowcraft.generator.process.Process attribute)
main_raw_inputs (flowcraft.generator.engine.NextflowGenerator attribute)
MainWrapper (class in flowcraft.templates.flowcraft_utils.flowcraft_base)
MappingPatlas (class in flowcraft.generator.components.patlas_mapping)
MashDist (class in flowcraft.generator.components.distance_estimation)
MashScreen (class in flowcraft.generator.components.distance_estimation)
MashSketchFasta (class in flowcraft.generator.components.distance_estimation)
MashSketchFastq (class in flowcraft.generator.components.distance_estimation)
Maxbin2 (class in flowcraft.generator.components.metagenomics)
Megahit (class in flowcraft.generator.components.metagenomics)
merge_default_adapters() (in module flowcraft.templates.trimmomatic)
merge_params (flowcraft.generator.engine.NextflowGenerator attribute)
Metabat2 (class in flowcraft.generator.components.metagenomics)
Metamlst (class in flowcraft.generator.components.mlst)
Metaprob (class in flowcraft.generator.components.metagenomics)
Metaspades (class in flowcraft.generator.components.metagenomics)
Midas_species (class in flowcraft.generator.components.metagenomics)
min_gc (flowcraft.templates.process_assembly.Assembly attribute)
Mlst (class in flowcraft.generator.components.mlst)
Momps (class in flowcraft.generator.components.typing)
N
NextflowGenerator (class in flowcraft.generator.engine)
nf_file (flowcraft.generator.engine.NextflowGenerator attribute)
O
output_channel (flowcraft.generator.process.Process attribute)
output_type (flowcraft.generator.process.Process attribute)
P
param_id (flowcraft.generator.process.Process attribute)
params (flowcraft.generator.engine.NextflowGenerator attribute)
(flowcraft.generator.process.Process attribute)
parse_coverage_table() (in module flowcraft.templates.process_assembly_mapping)
parse_files() (flowcraft.templates.process_abricate.Abricate method)
parse_log() (in module flowcraft.templates.trimmomatic)
(in module flowcraft.templates.trimmomatic_report)
parse_pipeline() (in module flowcraft.generator.pipeline_parser)
PathoTyping (class in flowcraft.generator.components.typing)
PatlasConsensus (class in flowcraft.generator.process)
pid (flowcraft.generator.process.Process attribute)
Pilon (class in flowcraft.generator.components.assembly_processing)
pipeline_name (flowcraft.generator.engine.NextflowGenerator attribute)
pipeline_str (flowcraft.generator.recipe.Recipe attribute)
pipeline_string (flowcraft.generator.recipe.InnuendoRecipe attribute)
proc_collector() (in module flowcraft.generator.process_details)
Process (class in flowcraft.generator.process)
process_map (flowcraft.generator.engine.NextflowGenerator attribute)
process_to_id (flowcraft.generator.recipe.InnuendoRecipe attribute)
ProcessError
processes (flowcraft.generator.engine.NextflowGenerator attribute)
ProcessSkesa (class in flowcraft.generator.components.assembly_processing)
ProcessSpades (class in flowcraft.generator.components.assembly_processing)
procs_dict_parser() (in module flowcraft.generator.process_details)
Prokka (class in flowcraft.generator.components.annotation)
Q
Quast (class in flowcraft.generator.components.assembly_processing)
R
RANGES (in module flowcraft.templates.integrity_coverage)
RAW_MAPPING (flowcraft.generator.process.Process attribute)
ReadsDownload (class in flowcraft.generator.components.downloads)
Recipe (class in flowcraft.generator.recipe)
RecipeError
remove_inner_forks() (in module flowcraft.generator.pipeline_parser)
remove_unique_identifiers() (in module flowcraft.generator.pipeline_parser)
RemoveHost (class in flowcraft.generator.components.metagenomics)
render() (flowcraft.generator.process.Process static method)
render_pipeline() (flowcraft.generator.engine.NextflowGenerator method)
report (flowcraft.templates.process_assembly.Assembly attribute)
ReportCompiler (class in flowcraft.generator.process)
ReportError
resources (flowcraft.generator.engine.NextflowGenerator attribute)
run_auto_pipeline() (flowcraft.generator.recipe.InnuendoRecipe method)
S
sample (flowcraft.templates.assembly_report.Assembly attribute)
(flowcraft.templates.process_assembly.Assembly attribute)
SanityError
secondary_channels (flowcraft.generator.engine.NextflowGenerator attribute)
secondary_inputs (flowcraft.generator.process.Process attribute)
send_to_output() (in module flowcraft.templates.mashdist2json)
SeqTyping (class in flowcraft.generator.components.typing)
Seroba (class in flowcraft.generator.components.typing)
set_channels() (flowcraft.generator.process.Process method)
set_compiler_channels() (flowcraft.generator.process.Compiler method)
set_extra_inputs() (flowcraft.generator.process.Init method)
set_kmers() (in module flowcraft.templates.megahit)
(in module flowcraft.templates.metaspades)
(in module flowcraft.templates.spades)
set_main_channel_names() (flowcraft.generator.process.Process method)
set_param_id() (flowcraft.generator.process.Process method)
set_raw_inputs() (flowcraft.generator.process.Init method)
set_secondary_channel() (flowcraft.generator.process.Process method)
set_secondary_inputs() (flowcraft.generator.process.Init method)
Sistr (class in flowcraft.generator.components.typing)
Skesa (class in flowcraft.generator.components.assembly)
skip_class (flowcraft.generator.engine.NextflowGenerator attribute)
Spades (class in flowcraft.generator.components.assembly)
SplitAssembly (class in flowcraft.generator.components.metagenomics)
start_proc_insanity_check() (in module flowcraft.generator.pipeline_parser)
status_channels (flowcraft.generator.components.reads_quality_control.Fastqc attribute)
(flowcraft.generator.engine.NextflowGenerator attribute)
(flowcraft.generator.process.Process attribute)
status_strs (flowcraft.generator.process.Process attribute)
StatusCompiler (class in flowcraft.generator.process)
storage (flowcraft.templates.process_abricate.Abricate attribute)
summary_info (flowcraft.templates.assembly_report.Assembly attribute)
T
template (flowcraft.generator.engine.NextflowGenerator attribute)
(flowcraft.generator.process.Process attribute)
template_str (flowcraft.generator.process.Process attribute)
test_get_lanes() (in module flowcraft.tests.test_pipeline_parser)
test_get_source_lane() (in module flowcraft.tests.test_pipeline_parser)
test_get_source_lane_2() (in module flowcraft.tests.test_pipeline_parser)
test_linear_connection() (in module flowcraft.tests.test_pipeline_parser)
test_linear_lane_connection() (in module flowcraft.tests.test_pipeline_parser)
test_linear_multi_lane_connection() (in module flowcraft.tests.test_pipeline_parser)
test_multi_fork_connection() (in module flowcraft.tests.test_pipeline_parser)
test_parse_pipeline() (in module flowcraft.tests.test_pipeline_parser)
test_parse_pipeline_file() (in module flowcraft.tests.test_pipeline_parser)
test_remove_id() (in module flowcraft.tests.test_pipeline_parser)
test_two_fork_connection() (in module flowcraft.tests.test_pipeline_parser)
test_two_fork_connection_mismatch_lane() (in module flowcraft.tests.test_pipeline_parser)
test_unique_id_len() (in module flowcraft.tests.test_pipeline_parser)
trim_range() (in module flowcraft.templates.fastqc_report)
Trimmomatic (class in flowcraft.generator.components.reads_quality_control)
trimmomatic_log() (in module flowcraft.templates.trimmomatic)
TrueCoverage (class in flowcraft.generator.components.reads_quality_control)
U
Unicycler (class in flowcraft.generator.components.assembly)
update_attributes() (flowcraft.generator.process.Process method)
update_main_forks() (flowcraft.generator.process.Process method)
update_main_input() (flowcraft.generator.process.Process method)
user_config (flowcraft.generator.engine.NextflowGenerator attribute)
V
validate_pipeline() (flowcraft.generator.recipe.InnuendoRecipe static method)
ViralAssembly (class in flowcraft.generator.components.assembly)
W
write_assembly() (flowcraft.templates.process_assembly.Assembly method)
write_configs() (flowcraft.generator.engine.NextflowGenerator method)
write_json_report() (in module flowcraft.templates.fastqc_report)
write_report() (flowcraft.templates.process_assembly.Assembly method)
(in module flowcraft.templates.trimmomatic)
(in module flowcraft.templates.trimmomatic_report)
write_report_data() (flowcraft.templates.process_abricate.AbricateReport method)
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