SNAPPY Pipeline
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Pipeline Users Docs
Quickstart
Installation
Usage
Overview
Pipeline Step Docs
Pipeline Step Introduction
Generic Pipeline Step Description
Adapter Trimming
Germline Build Target Sequence gCNV Model
Germline Build WGS gCNV Model
HLA Typing
IGV Session Generation
NGS Data QC
NGS Mapping
NGS Sanity Checking
Somatic Gene Fusion Calling
Somatic Neoepitope Prediction
Somatic NGS Sanity Checking
Somatic Purity & Ploidy Estimate
Somatic Targeted Seq. CNV Calling
Somatic Variant Annotation
Somatic Variant Calling
Somatic Variant Checking
Somatic Variant Expression
Somatic Variant Filtration
Somatic WGS CNV Calling
Somatic WGS SV Calling
Germline Targeted Seq. CNV Calling
Germline Targeted Seq. MEI Calling
Germline Repeat Expansion Analysis
T cell CRG Report
Germline Variant Annotation
Germline Variant Calling
Germline Variant Sanity Checking
Germline Variant
De Novo
Filtration
Germline Variant Phasing
Germline Variant Filtration
Germline SV Calling
Germline WGS SV Filtration
Pipeline Developers Docs
Developer’s Introduction
Somatic Variant Calling Dissection
NGS Mapping Dissection
API Documentation
Project Info
Contributing
How To: Release
Credits
Changelog
License
SNAPPY Pipeline
Index
Edit on GitHub
Index
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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R
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W
A
actions (snappy_pipeline.workflows.abstract.BaseStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInBaiExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInBamExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInVcfExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.WritePedigreeStepPart attribute)
B
base_folder (snappy_pipeline.find_file.FileSystemCrawlerResult attribute)
base_paths (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
BaseStep (class in snappy_pipeline.workflows.abstract)
BaseStepPart (class in snappy_pipeline.workflows.abstract)
C
cache (snappy_pipeline.find_file.FileSystemCrawler attribute)
cache_dirty (snappy_pipeline.find_file.FileSystemCrawler attribute)
cache_file_name (snappy_pipeline.workflows.abstract.LinkInPathGenerator attribute)
cache_invalidated (snappy_pipeline.find_file.FileSystemCrawler attribute)
cache_path (snappy_pipeline.find_file.FileSystemCrawler attribute)
check_config() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
config_lookup_paths (snappy_pipeline.workflows.abstract.BaseStep attribute)
config_paths (snappy_pipeline.workflows.abstract.BaseStep attribute)
(snappy_pipeline.workflows.abstract.LinkInPathGenerator attribute)
D
DataSearchInfo (class in snappy_pipeline.workflows.abstract)
DataSetInfo (class in snappy_pipeline.workflows.abstract)
default_config_yaml() (snappy_pipeline.workflows.abstract.BaseStep class method)
default_resource_usage (snappy_pipeline.workflows.abstract.BaseStepPart attribute)
dictify() (in module snappy_pipeline.utils)
DictQuery (class in snappy_pipeline.utils)
disable_patterns (snappy_pipeline.workflows.abstract.LinkOutStepPart attribute)
E
ensure_w_config() (snappy_pipeline.workflows.abstract.BaseStep method)
expand_ref() (in module snappy_pipeline.base)
ext_names (snappy_pipeline.workflows.abstract.InputFilesStepPartMixin attribute)
ext_values (snappy_pipeline.workflows.abstract.InputFilesStepPartMixin attribute)
F
FileNamesTooDifferent
files (snappy_pipeline.find_file.FileSystemCrawlerResult attribute)
FileSystemCrawler (class in snappy_pipeline.find_file)
FileSystemCrawlerResult (class in snappy_pipeline.find_file)
flatten() (in module snappy_pipeline.utils)
G
get() (snappy_pipeline.utils.DictQuery method)
get_args() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
get_default_partition() (snappy_pipeline.workflows.abstract.BaseStepPart static method)
get_input_files() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
(snappy_pipeline.workflows.abstract.LinkInStep method)
(snappy_pipeline.workflows.abstract.LinkOutStepPart method)
(snappy_pipeline.workflows.abstract.WritePedigreeStepPart method)
get_log_file() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
get_ngs_library_folder_name() (in module snappy_pipeline.workflows.abstract)
get_output_files() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
(snappy_pipeline.workflows.abstract.LinkInStep method)
(snappy_pipeline.workflows.abstract.LinkOutStepPart method)
(snappy_pipeline.workflows.abstract.WritePedigreeStepPart method)
get_params() (snappy_pipeline.workflows.abstract.BaseStep method)
get_resource() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
get_resource_usage() (snappy_pipeline.workflows.abstract.BaseStepPart method)
get_result_files() (snappy_pipeline.workflows.abstract.BaseStep method)
get_shell_cmd() (snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
(snappy_pipeline.workflows.abstract.LinkInStep method)
(snappy_pipeline.workflows.abstract.LinkInVcfExternalStepPart method)
(snappy_pipeline.workflows.abstract.LinkOutStepPart method)
get_tmpdir() (snappy_pipeline.workflows.abstract.BaseStep method)
I
ImplementationUnavailableError
include_ped_file (snappy_pipeline.workflows.abstract.InputFilesStepPartMixin attribute)
InputFilesStepPartMixin (class in snappy_pipeline.workflows.abstract)
invalidation_paths (snappy_pipeline.find_file.FileSystemCrawler attribute)
InvalidConfiguration
is_background (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
is_none() (in module snappy_pipeline.utils)
is_not_none() (in module snappy_pipeline.utils)
L
LinkInBaiExternalStepPart (class in snappy_pipeline.workflows.abstract)
LinkInBamExternalStepPart (class in snappy_pipeline.workflows.abstract)
LinkInPathGenerator (class in snappy_pipeline.workflows.abstract)
LinkInStep (class in snappy_pipeline.workflows.abstract)
LinkInVcfExternalStepPart (class in snappy_pipeline.workflows.abstract)
LinkOutStepPart (class in snappy_pipeline.workflows.abstract)
listify() (in module snappy_pipeline.utils)
lock_timeout (snappy_pipeline.find_file.FileSystemCrawler attribute)
logger (snappy_pipeline.find_file.FileSystemCrawler attribute)
M
merge_dicts() (in module snappy_pipeline.base)
merge_kwargs() (in module snappy_pipeline.base)
MissingConfiguration
mixed_se_pe (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
modified_environ() (in module snappy_pipeline.workflows.abstract)
module
snappy_pipeline.base
snappy_pipeline.find_file
snappy_pipeline.utils
snappy_pipeline.workflows.abstract
snappy_pipeline.workflows.adapter_trimming
snappy_pipeline.workflows.helper_gcnv_model_targeted
snappy_pipeline.workflows.helper_gcnv_model_wgs
snappy_pipeline.workflows.hla_typing
snappy_pipeline.workflows.igv_session_generation
snappy_pipeline.workflows.ngs_data_qc
snappy_pipeline.workflows.ngs_mapping
snappy_pipeline.workflows.ngs_sanity_checking
snappy_pipeline.workflows.panel_of_normals
snappy_pipeline.workflows.repeat_expansion
snappy_pipeline.workflows.somatic_gene_fusion_calling
snappy_pipeline.workflows.somatic_neoepitope_prediction
snappy_pipeline.workflows.somatic_ngs_sanity_checking
snappy_pipeline.workflows.somatic_purity_ploidy_estimate
snappy_pipeline.workflows.somatic_targeted_seq_cnv_calling
snappy_pipeline.workflows.somatic_variant_annotation
snappy_pipeline.workflows.somatic_variant_calling
snappy_pipeline.workflows.somatic_variant_checking
snappy_pipeline.workflows.somatic_variant_expression
snappy_pipeline.workflows.somatic_variant_filtration
snappy_pipeline.workflows.somatic_wgs_cnv_calling
snappy_pipeline.workflows.somatic_wgs_sv_calling
snappy_pipeline.workflows.sv_calling_targeted
snappy_pipeline.workflows.sv_calling_wgs
snappy_pipeline.workflows.targeted_seq_mei_calling
snappy_pipeline.workflows.tcell_crg_report
snappy_pipeline.workflows.variant_annotation
snappy_pipeline.workflows.variant_calling
snappy_pipeline.workflows.variant_checking
snappy_pipeline.workflows.variant_denovo_filtration
snappy_pipeline.workflows.variant_filtration
snappy_pipeline.workflows.variant_phasing
N
name (snappy_pipeline.workflows.abstract.BaseStep attribute)
(snappy_pipeline.workflows.abstract.DataSetInfo attribute)
(snappy_pipeline.workflows.abstract.LinkInBaiExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInBamExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInVcfExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.WritePedigreeSampleNameStepPart attribute)
(snappy_pipeline.workflows.abstract.WritePedigreeStepPart attribute)
named_files (snappy_pipeline.find_file.FileSystemCrawlerResult attribute)
named_patterns (snappy_pipeline.find_file.PatternSet attribute)
names (snappy_pipeline.find_file.FileSystemCrawlerResult attribute)
(snappy_pipeline.find_file.PatternSet attribute)
P
pattern_set_keys (snappy_pipeline.workflows.abstract.LinkInBaiExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInBamExternalStepPart attribute)
(snappy_pipeline.workflows.abstract.LinkInVcfExternalStepPart attribute)
patterns (snappy_pipeline.find_file.PatternSet attribute)
PatternSet (class in snappy_pipeline.find_file)
pedigree_field_kwargs (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
prev_class (snappy_pipeline.workflows.abstract.InputFilesStepPartMixin attribute)
previous_steps (snappy_pipeline.workflows.abstract.BaseStep attribute)
print_config() (in module snappy_pipeline.base)
print_sample_sheets() (in module snappy_pipeline.base)
R
register_sub_step_classes() (snappy_pipeline.workflows.abstract.BaseStep method)
register_sub_workflow() (snappy_pipeline.workflows.abstract.BaseStep method)
require_dna_ngs_library (snappy_pipeline.workflows.abstract.WritePedigreeStepPart attribute)
resource_usage (snappy_pipeline.workflows.abstract.BaseStepPart attribute)
run() (snappy_pipeline.find_file.FileSystemCrawler method)
(snappy_pipeline.workflows.abstract.BaseStep method)
(snappy_pipeline.workflows.abstract.BaseStepPart method)
(snappy_pipeline.workflows.abstract.LinkInPathGenerator method)
(snappy_pipeline.workflows.abstract.LinkInStep method)
(snappy_pipeline.workflows.abstract.WritePedigreeSampleNameStepPart method)
(snappy_pipeline.workflows.abstract.WritePedigreeStepPart method)
S
save_cache() (snappy_pipeline.find_file.FileSystemCrawler method)
search_paths (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
search_patterns (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
sheet (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
sheet_path (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
sheet_shortcut_args (snappy_pipeline.workflows.abstract.BaseStep attribute)
sheet_shortcut_class (snappy_pipeline.workflows.abstract.BaseStep attribute)
sheet_shortcut_kwargs (snappy_pipeline.workflows.abstract.BaseStep attribute)
sheets (snappy_pipeline.workflows.abstract.BaseStep attribute)
shortcut_sheets (snappy_pipeline.workflows.abstract.BaseStep attribute)
SkipLibraryWarning
snakefile_path() (in module snappy_pipeline.base)
snappy_pipeline.base
module
snappy_pipeline.find_file
module
snappy_pipeline.utils
module
snappy_pipeline.workflows.abstract
module
snappy_pipeline.workflows.adapter_trimming
module
snappy_pipeline.workflows.helper_gcnv_model_targeted
module
snappy_pipeline.workflows.helper_gcnv_model_wgs
module
snappy_pipeline.workflows.hla_typing
module
snappy_pipeline.workflows.igv_session_generation
module
snappy_pipeline.workflows.ngs_data_qc
module
snappy_pipeline.workflows.ngs_mapping
module
snappy_pipeline.workflows.ngs_sanity_checking
module
snappy_pipeline.workflows.panel_of_normals
module
snappy_pipeline.workflows.repeat_expansion
module
snappy_pipeline.workflows.somatic_gene_fusion_calling
module
snappy_pipeline.workflows.somatic_neoepitope_prediction
module
snappy_pipeline.workflows.somatic_ngs_sanity_checking
module
snappy_pipeline.workflows.somatic_purity_ploidy_estimate
module
snappy_pipeline.workflows.somatic_targeted_seq_cnv_calling
module
snappy_pipeline.workflows.somatic_variant_annotation
module
snappy_pipeline.workflows.somatic_variant_calling
module
snappy_pipeline.workflows.somatic_variant_checking
module
snappy_pipeline.workflows.somatic_variant_expression
module
snappy_pipeline.workflows.somatic_variant_filtration
module
snappy_pipeline.workflows.somatic_wgs_cnv_calling
module
snappy_pipeline.workflows.somatic_wgs_sv_calling
module
snappy_pipeline.workflows.sv_calling_targeted
module
snappy_pipeline.workflows.sv_calling_wgs
module
snappy_pipeline.workflows.targeted_seq_mei_calling
module
snappy_pipeline.workflows.tcell_crg_report
module
snappy_pipeline.workflows.variant_annotation
module
snappy_pipeline.workflows.variant_calling
module
snappy_pipeline.workflows.variant_checking
module
snappy_pipeline.workflows.variant_denovo_filtration
module
snappy_pipeline.workflows.variant_filtration
module
snappy_pipeline.workflows.variant_phasing
module
sodar_title (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
sodar_uuid (snappy_pipeline.workflows.abstract.DataSetInfo attribute)
STDERR_TO_LOG_FILE (in module snappy_pipeline.workflows.abstract)
sub_workflows (snappy_pipeline.workflows.abstract.BaseStep attribute)
substep_dispatch() (snappy_pipeline.workflows.abstract.BaseStep method)
substep_getattr() (snappy_pipeline.workflows.abstract.BaseStep method)
T
to_dict() (snappy_pipeline.find_file.FileSystemCrawlerResult method)
try_or_none() (in module snappy_pipeline.utils)
U
UnknownFiltrationSourceException
UnsupportedActionException
W
w_config (snappy_pipeline.workflows.abstract.BaseStep attribute)
work_dir (snappy_pipeline.workflows.abstract.BaseStep attribute)
(snappy_pipeline.workflows.abstract.LinkInPathGenerator attribute)
workflow (snappy_pipeline.workflows.abstract.BaseStep attribute)
wrapper_path() (snappy_pipeline.workflows.abstract.BaseStep class method)
WritePedigreeSampleNameStepPart (class in snappy_pipeline.workflows.abstract)
WritePedigreeStepPart (class in snappy_pipeline.workflows.abstract)
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