Assemblerflow
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assemblerflow package
Assemblerflow
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B
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C
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D
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_
_add_dependency() (assemblerflow.generator.engine.NextflowGenerator method)
_build_connections() (assemblerflow.generator.engine.NextflowGenerator method)
_build_footer() (assemblerflow.generator.engine.NextflowGenerator method)
_build_header() (assemblerflow.generator.engine.NextflowGenerator method)
_context (assemblerflow.generator.process.Process attribute)
_fork_tree (assemblerflow.generator.engine.NextflowGenerator attribute)
_get_container_string() (assemblerflow.generator.engine.NextflowGenerator static method)
_get_fork_tree() (assemblerflow.generator.engine.NextflowGenerator method)
_get_params_help() (assemblerflow.generator.engine.NextflowGenerator method)
_get_params_string() (assemblerflow.generator.engine.NextflowGenerator method)
_get_process_names() (assemblerflow.generator.engine.NextflowGenerator method)
_get_resources_string() (assemblerflow.generator.engine.NextflowGenerator static method)
_parse_process_name() (assemblerflow.generator.engine.NextflowGenerator static method)
_render_config() (assemblerflow.generator.engine.NextflowGenerator static method)
_search_tree_backwards() (assemblerflow.generator.engine.NextflowGenerator method)
_set_channels() (assemblerflow.generator.engine.NextflowGenerator method)
_set_compiler_channels() (assemblerflow.generator.engine.NextflowGenerator method)
_set_configurations() (assemblerflow.generator.engine.NextflowGenerator method)
_set_general_compilers() (assemblerflow.generator.engine.NextflowGenerator method)
_set_implicit_link() (assemblerflow.generator.engine.NextflowGenerator method)
_set_init_process() (assemblerflow.generator.engine.NextflowGenerator method)
_set_secondary_channels() (assemblerflow.generator.engine.NextflowGenerator method)
_set_status_channels() (assemblerflow.generator.engine.NextflowGenerator method)
_set_template() (assemblerflow.generator.process.Process method)
_template_path (assemblerflow.generator.process.Process attribute)
_test_connection() (assemblerflow.generator.engine.NextflowGenerator static method)
_update_extra_inputs() (assemblerflow.generator.engine.NextflowGenerator method)
_update_raw_input() (assemblerflow.generator.engine.NextflowGenerator method)
_update_secondary_channels() (assemblerflow.generator.engine.NextflowGenerator method)
_update_secondary_inputs() (assemblerflow.generator.engine.NextflowGenerator method)
A
Abricate (class in assemblerflow.generator.components.annotation)
(class in assemblerflow.templates.process_abricate)
AbricateReport (class in assemblerflow.templates.process_abricate)
assemblerflow (module)
assemblerflow.assemblerflow (module)
assemblerflow.generator (module)
assemblerflow.generator.components (module)
assemblerflow.generator.components.annotation (module)
assemblerflow.generator.components.assembly (module)
assemblerflow.generator.components.assembly_processing (module)
assemblerflow.generator.components.distance_estimation (module)
assemblerflow.generator.components.downloads (module)
assemblerflow.generator.components.reads_quality_control (module)
assemblerflow.generator.engine (module)
assemblerflow.generator.error_handling (module)
assemblerflow.generator.header_skeleton (module)
assemblerflow.generator.pipeline_parser (module)
assemblerflow.generator.process (module)
assemblerflow.generator.process_details (module)
assemblerflow.templates (module)
assemblerflow.templates.assembly_report (module)
assemblerflow.templates.fastqc (module)
assemblerflow.templates.fastqc_report (module)
assemblerflow.templates.integrity_coverage (module)
assemblerflow.templates.mapping2json (module)
assemblerflow.templates.mashdist2json (module)
assemblerflow.templates.mashscreen2json (module)
assemblerflow.templates.pATLAS_consensus_json (module)
assemblerflow.templates.pipeline_status (module)
assemblerflow.templates.process_abricate (module)
assemblerflow.templates.process_assembly_mapping (module)
assemblerflow.templates.spades (module)
assemblerflow.templates.trimmomatic (module)
assemblerflow.templates.trimmomatic_report (module)
assemblerflow.tests (module)
Assembly (class in assemblerflow.templates.assembly_report)
AssemblyMapping (class in assemblerflow.generator.components.assembly_processing)
B
brackets_but_no_lanes() (in module assemblerflow.generator.pipeline_parser)
brackets_insanity_check() (in module assemblerflow.generator.pipeline_parser)
build() (assemblerflow.generator.engine.NextflowGenerator method)
(in module assemblerflow.assemblerflow)
C
check_filtered_assembly() (in module assemblerflow.templates.process_assembly_mapping)
check_summary_health() (in module assemblerflow.templates.fastqc_report)
CheckCoverage (class in assemblerflow.generator.components.reads_quality_control)
clean_up() (in module assemblerflow.templates.trimmomatic)
colored_print() (in module assemblerflow.generator.process_details)
compiler (assemblerflow.generator.process.Process attribute)
Compiler (class in assemblerflow.generator.process)
compilers (assemblerflow.generator.engine.NextflowGenerator attribute)
containers (assemblerflow.generator.engine.NextflowGenerator attribute)
contig_boundaries (assemblerflow.templates.assembly_report.Assembly attribute)
contig_coverage (assemblerflow.templates.assembly_report.Assembly attribute)
contigs (assemblerflow.templates.assembly_report.Assembly attribute)
convert_adatpers() (in module assemblerflow.templates.fastqc)
copy_project() (in module assemblerflow.assemblerflow)
D
dependencies (assemblerflow.generator.process.Process attribute)
depthfilereader() (in module assemblerflow.templates.mapping2json)
directives (assemblerflow.generator.process.Process attribute)
DownloadReads (class in assemblerflow.generator.components.downloads)
E
empty_tasks() (in module assemblerflow.generator.pipeline_parser)
evaluate_min_coverage() (in module assemblerflow.templates.process_assembly_mapping)
extra_input (assemblerflow.generator.process.Process attribute)
extra_inputs (assemblerflow.generator.engine.NextflowGenerator attribute)
F
FastQC (class in assemblerflow.generator.components.reads_quality_control)
FastqcTrimmomatic (class in assemblerflow.generator.components.reads_quality_control)
filter_assembly() (in module assemblerflow.templates.process_assembly_mapping)
filter_bam() (in module assemblerflow.templates.process_assembly_mapping)
final_char_insanity_check() (in module assemblerflow.generator.pipeline_parser)
fork_connection() (in module assemblerflow.generator.pipeline_parser)
fork_procs_insanity_check() (in module assemblerflow.generator.pipeline_parser)
forks (assemblerflow.generator.process.Process attribute)
G
get_args() (in module assemblerflow.assemblerflow)
get_assembly_size() (in module assemblerflow.templates.process_assembly_mapping)
get_coverage_from_file() (in module assemblerflow.templates.process_assembly_mapping)
get_coverage_sliding() (assemblerflow.templates.assembly_report.Assembly method)
get_encodings_in_range() (in module assemblerflow.templates.integrity_coverage)
get_filter() (assemblerflow.templates.process_abricate.Abricate method)
get_gc_sliding() (assemblerflow.templates.assembly_report.Assembly method)
get_json_info() (in module assemblerflow.templates.pipeline_status)
get_lanes() (in module assemblerflow.generator.pipeline_parser)
get_plot_data() (assemblerflow.templates.process_abricate.AbricateReport method)
get_previous_stats() (in module assemblerflow.templates.pipeline_status)
get_qual_range() (in module assemblerflow.templates.integrity_coverage)
get_sample_trim() (in module assemblerflow.templates.fastqc_report)
get_source_lane() (in module assemblerflow.generator.pipeline_parser)
get_summary() (in module assemblerflow.templates.fastqc_report)
get_summary_stats() (assemblerflow.templates.assembly_report.Assembly method)
get_table_data() (assemblerflow.templates.process_abricate.AbricateReport method)
get_trim_index() (in module assemblerflow.templates.fastqc_report)
get_user_channel() (assemblerflow.generator.process.Process method)
guess_file_compression() (in module assemblerflow.templates.integrity_coverage)
I
ignore_pid (assemblerflow.generator.process.Process attribute)
ignore_type (assemblerflow.generator.process.Process attribute)
Init (class in assemblerflow.generator.process)
inner_fork_insanity_checks() (in module assemblerflow.generator.pipeline_parser)
input_channel (assemblerflow.generator.process.Process attribute)
input_type (assemblerflow.generator.process.Process attribute)
input_user_channel (assemblerflow.generator.process.Process attribute)
insanity_checks() (in module assemblerflow.generator.pipeline_parser)
IntegrityCoverage (class in assemblerflow.generator.components.reads_quality_control)
iter_filter() (assemblerflow.templates.process_abricate.Abricate method)
L
lane_char_insanity_check() (in module assemblerflow.generator.pipeline_parser)
lanes (assemblerflow.generator.engine.NextflowGenerator attribute)
late_proc_insanity_check() (in module assemblerflow.generator.pipeline_parser)
linear_connection() (in module assemblerflow.generator.pipeline_parser)
linear_lane_connection() (in module assemblerflow.generator.pipeline_parser)
link_end (assemblerflow.generator.process.Process attribute)
link_start (assemblerflow.generator.process.Process attribute)
M
MAGIC_DICT (in module assemblerflow.templates.integrity_coverage)
main() (in module assemblerflow.assemblerflow)
(in module assemblerflow.templates.pipeline_status)
main_forks (assemblerflow.generator.process.Process attribute)
main_raw_inputs (assemblerflow.generator.engine.NextflowGenerator attribute)
merge_default_adapters() (in module assemblerflow.templates.trimmomatic)
N
NextflowGenerator (class in assemblerflow.generator.engine)
nf_file (assemblerflow.generator.engine.NextflowGenerator attribute)
O
output_channel (assemblerflow.generator.process.Process attribute)
output_type (assemblerflow.generator.process.Process attribute)
P
params (assemblerflow.generator.engine.NextflowGenerator attribute)
(assemblerflow.generator.process.Process attribute)
parse_coverage_table() (in module assemblerflow.templates.process_assembly_mapping)
parse_files() (assemblerflow.templates.process_abricate.Abricate method)
parse_log() (in module assemblerflow.templates.trimmomatic)
(in module assemblerflow.templates.trimmomatic_report)
parse_pipeline() (in module assemblerflow.generator.pipeline_parser)
PatlasConsensus (class in assemblerflow.generator.process)
PatlasMashDist (class in assemblerflow.generator.components.distance_estimation)
PatlasMashScreen (class in assemblerflow.generator.components.distance_estimation)
pid (assemblerflow.generator.process.Process attribute)
Pilon (class in assemblerflow.generator.components.assembly_processing)
pipeline_name (assemblerflow.generator.engine.NextflowGenerator attribute)
proc_collector() (in module assemblerflow.generator.process_details)
Process (class in assemblerflow.generator.process)
process_map (in module assemblerflow.generator.engine)
ProcessError
processes (assemblerflow.generator.engine.NextflowGenerator attribute)
ProcessSkesa (class in assemblerflow.generator.components.assembly_processing)
ProcessSpades (class in assemblerflow.generator.components.assembly_processing)
procs_dict_parser() (in module assemblerflow.generator.process_details)
Prokka (class in assemblerflow.generator.components.annotation)
R
RANGES (in module assemblerflow.templates.integrity_coverage)
RAW_MAPPING (assemblerflow.generator.process.Process attribute)
remove_inner_forks() (in module assemblerflow.generator.pipeline_parser)
render() (assemblerflow.generator.process.Process static method)
render_pipeline() (assemblerflow.generator.engine.NextflowGenerator method)
ReportCompiler (class in assemblerflow.generator.process)
resources (assemblerflow.generator.engine.NextflowGenerator attribute)
S
sample (assemblerflow.templates.assembly_report.Assembly attribute)
SanityError
secondary_channels (assemblerflow.generator.engine.NextflowGenerator attribute)
secondary_inputs (assemblerflow.generator.engine.NextflowGenerator attribute)
(assemblerflow.generator.process.Process attribute)
send_to_output() (in module assemblerflow.templates.mashdist2json)
set_channels() (assemblerflow.generator.process.Process method)
set_compiler_channels() (assemblerflow.generator.process.Compiler method)
set_extra_inputs() (assemblerflow.generator.process.Init method)
set_kmers() (in module assemblerflow.templates.spades)
set_main_channel_names() (assemblerflow.generator.process.Process method)
set_raw_inputs() (assemblerflow.generator.process.Init method)
set_secondary_channel() (assemblerflow.generator.process.Process method)
set_secondary_inputs() (assemblerflow.generator.process.Init method)
Skesa (class in assemblerflow.generator.components.assembly)
skip_class (assemblerflow.generator.engine.NextflowGenerator attribute)
Spades (class in assemblerflow.generator.components.assembly)
start_proc_insanity_check() (in module assemblerflow.generator.pipeline_parser)
status_channels (assemblerflow.generator.components.reads_quality_control.FastQC attribute)
(assemblerflow.generator.engine.NextflowGenerator attribute)
(assemblerflow.generator.process.Process attribute)
status_strs (assemblerflow.generator.process.Process attribute)
StatusCompiler (class in assemblerflow.generator.process)
storage (assemblerflow.templates.process_abricate.Abricate attribute)
summary_info (assemblerflow.templates.assembly_report.Assembly attribute)
T
template (assemblerflow.generator.engine.NextflowGenerator attribute)
(assemblerflow.generator.process.Process attribute)
template_str (assemblerflow.generator.process.Process attribute)
trim_range() (in module assemblerflow.templates.fastqc_report)
Trimmomatic (class in assemblerflow.generator.components.reads_quality_control)
trimmomatic_log() (in module assemblerflow.templates.trimmomatic)
TrueCoverage (class in assemblerflow.generator.components.reads_quality_control)
U
update_attributes() (assemblerflow.generator.process.Process method)
update_main_forks() (assemblerflow.generator.process.Process method)
update_main_input() (assemblerflow.generator.process.Process method)
user_config (assemblerflow.generator.engine.NextflowGenerator attribute)
V
validate_build_arguments() (in module assemblerflow.assemblerflow)
W
write_configs() (assemblerflow.generator.engine.NextflowGenerator method)
write_json_report() (in module assemblerflow.templates.fastqc_report)
write_report() (in module assemblerflow.templates.trimmomatic)
(in module assemblerflow.templates.trimmomatic_report)
write_report_data() (assemblerflow.templates.process_abricate.AbricateReport method)
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