FlowCraft
recipes
Getting Started
Overview
Installation
About
User Guide
Basic Usage
Pipeline building
Pipeline configuration
Pipeline inspection
Pipeline reports
Components
Developer Guide
General orientation
Process creation guidelines
Template creation guidelines
Recipe creation guidelines
Docker containers guidelines
Dotfiles
Pipeline reporting
Reports
Source API
flowcraft package
FlowCraft
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
E
|
F
|
G
|
I
|
L
|
M
|
P
|
R
|
S
|
T
|
W
A
add_unique_identifiers() (in module flowcraft.generator.pipeline_parser)
Assembly (class in flowcraft.templates.assembly_report)
B
brackets_but_no_lanes() (in module flowcraft.generator.pipeline_parser)
brackets_insanity_check() (in module flowcraft.generator.pipeline_parser)
build_versions() (flowcraft.templates.flowcraft_utils.flowcraft_base.MainWrapper method)
C
check_filtered_assembly() (in module flowcraft.templates.process_assembly_mapping)
check_summary_health() (in module flowcraft.templates.fastqc_report)
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)
contig_boundaries (flowcraft.templates.assembly_report.Assembly attribute)
contig_coverage (flowcraft.templates.assembly_report.Assembly attribute)
contigs (flowcraft.templates.assembly_report.Assembly attribute)
convert_adatpers() (in module flowcraft.templates.fastqc)
E
empty_tasks() (in module flowcraft.generator.pipeline_parser)
evaluate_min_coverage() (in module flowcraft.templates.process_assembly_mapping)
F
filter_assembly() (in module flowcraft.templates.process_assembly_mapping)
filter_bam() (in module flowcraft.templates.process_assembly_mapping)
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.error_handling (module)
flowcraft.generator.footer_skeleton (module)
flowcraft.generator.header_skeleton (module)
flowcraft.generator.pipeline_parser (module)
flowcraft.generator.process_details (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.mashdist2json (module)
flowcraft.templates.megahit (module)
flowcraft.templates.metaspades (module)
flowcraft.templates.pATLAS_consensus_json (module)
flowcraft.templates.pipeline_status (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)
G
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_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_previous_stats() (in module flowcraft.templates.pipeline_status)
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_trim_index() (in module flowcraft.templates.fastqc_report)
guess_process() (in module flowcraft.generator.pipeline_parser)
I
inner_fork_insanity_checks() (in module flowcraft.generator.pipeline_parser)
insanity_checks() (in module flowcraft.generator.pipeline_parser)
InspectionError
is_odd() (in module flowcraft.templates.megahit)
L
lane_char_insanity_check() (in module flowcraft.generator.pipeline_parser)
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)
log_error() (in module flowcraft.templates.flowcraft_utils.flowcraft_base)
M
MainWrapper (class in flowcraft.templates.flowcraft_utils.flowcraft_base)
merge_default_adapters() (in module flowcraft.templates.trimmomatic)
P
parse_coverage_table() (in module flowcraft.templates.process_assembly_mapping)
parse_log() (in module flowcraft.templates.trimmomatic)
(in module flowcraft.templates.trimmomatic_report)
parse_pipeline() (in module flowcraft.generator.pipeline_parser)
proc_collector() (in module flowcraft.generator.process_details)
ProcessError
procs_dict_parser() (in module flowcraft.generator.process_details)
R
RecipeError
remove_inner_forks() (in module flowcraft.generator.pipeline_parser)
remove_unique_identifiers() (in module flowcraft.generator.pipeline_parser)
ReportError
S
sample (flowcraft.templates.assembly_report.Assembly attribute)
SanityError
send_to_output() (in module flowcraft.templates.mashdist2json)
set_kmers() (in module flowcraft.templates.megahit)
(in module flowcraft.templates.metaspades)
(in module flowcraft.templates.spades)
start_proc_insanity_check() (in module flowcraft.generator.pipeline_parser)
summary_info (flowcraft.templates.assembly_report.Assembly attribute)
T
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_log() (in module flowcraft.templates.trimmomatic)
W
write_json_report() (in module flowcraft.templates.fastqc_report)
write_report() (in module flowcraft.templates.trimmomatic)
(in module flowcraft.templates.trimmomatic_report)
Read the Docs
v: recipes
Versions
latest
stable
recipes
dev
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.