Command Line Interface
usage: cubi-tk [-h] [--verbose] [--version]
{isa-tpl,isa-tab,snappy,sodar,sea-snap} ...
Positional Arguments
- cmd
Possible choices: isa-tpl, isa-tab, snappy, sodar, sea-snap
Named Arguments
- --version
show program’s version number and exit
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Sub-commands
isa-tpl
Create of ISA-tab directories from predefined templates.
cubi-tk isa-tpl [-h]
{bulk_rnaseq,generic,germline,mass_cytometry,microarray,ms_meta_biocrates,single_cell_rnaseq,somatic,stem_cell_core_bulk,stem_cell_core_sc}
...
Positional Arguments
- tpl
Possible choices: bulk_rnaseq, generic, germline, mass_cytometry, microarray, ms_meta_biocrates, single_cell_rnaseq, somatic, stem_cell_core_bulk, stem_cell_core_sc
Sub-commands
bulk_rnaseq
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl bulk_rnaseq [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var--measurement-types VAR__MEASUREMENT_TYPES]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var--technology-types VAR__TECHNOLOGY_TYPES]
[--var-lib-kit VAR_LIB_KIT]
[--var-organism VAR_ORGANISM]
[--var-batch VAR_BATCH]
[--var--lib-kits VAR__LIB_KITS]
[--var--organisms VAR__ORGANISMS]
[--var-instrument VAR_INSTRUMENT]
[--var-center-name VAR_CENTER_NAME]
[--var-center-contact VAR_CENTER_CONTACT]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-measurement-abbreviation VAR_A_MEASUREMENT_ABBREVIATION]
[--var-assay-name VAR_ASSAY_NAME]
[--var-sample-type VAR_SAMPLE_TYPE]
[--var-lib-strategy VAR_LIB_STRATEGY]
[--var-lib-selection VAR_LIB_SELECTION]
[--var-lib-layout VAR_LIB_LAYOUT]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-sample-names
template variables ‚sample_names‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var--measurement-types
template variables ‚_measurement_types‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var--technology-types
template variables ‚_technology_types‘
- --var-lib-kit
template variables ‚lib_kit‘
- --var-organism
template variables ‚organism‘
- --var-batch
template variables ‚batch‘
- --var--lib-kits
template variables ‚_lib_kits‘
- --var--organisms
template variables ‚_organisms‘
- --var-instrument
template variables ‚instrument‘
- --var-center-name
template variables ‚center_name‘
- --var-center-contact
template variables ‚center_contact‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-a-measurement-abbreviation
template variables ‚a_measurement_abbreviation‘
- --var-assay-name
template variables ‚assay_name‘
- --var-sample-type
template variables ‚sample_type‘
- --var-lib-strategy
template variables ‚lib_strategy‘
- --var-lib-selection
template variables ‚lib_selection‘
- --var-lib-layout
template variables ‚lib_layout‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
generic
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl generic [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var--measurement-types VAR__MEASUREMENT_TYPES]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var--technology-types VAR__TECHNOLOGY_TYPES]
[--var-lib-kit VAR_LIB_KIT]
[--var-organism VAR_ORGANISM] [--var-batch VAR_BATCH]
[--var--lib-kits VAR__LIB_KITS]
[--var--organisms VAR__ORGANISMS]
[--var-instrument VAR_INSTRUMENT]
[--var-center-name VAR_CENTER_NAME]
[--var-center-contact VAR_CENTER_CONTACT]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-measurement-abbreviation VAR_A_MEASUREMENT_ABBREVIATION]
[--var-assay-name VAR_ASSAY_NAME]
[--var-sample-type VAR_SAMPLE_TYPE]
[--var-lib-strategy VAR_LIB_STRATEGY]
[--var-lib-selection VAR_LIB_SELECTION]
[--var-lib-layout VAR_LIB_LAYOUT]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-sample-names
template variables ‚sample_names‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var--measurement-types
template variables ‚_measurement_types‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var--technology-types
template variables ‚_technology_types‘
- --var-lib-kit
template variables ‚lib_kit‘
- --var-organism
template variables ‚organism‘
- --var-batch
template variables ‚batch‘
- --var--lib-kits
template variables ‚_lib_kits‘
- --var--organisms
template variables ‚_organisms‘
- --var-instrument
template variables ‚instrument‘
- --var-center-name
template variables ‚center_name‘
- --var-center-contact
template variables ‚center_contact‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-a-measurement-abbreviation
template variables ‚a_measurement_abbreviation‘
- --var-assay-name
template variables ‚assay_name‘
- --var-sample-type
template variables ‚sample_type‘
- --var-lib-strategy
template variables ‚lib_strategy‘
- --var-lib-selection
template variables ‚lib_selection‘
- --var-lib-layout
template variables ‚lib_layout‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
germline
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl germline [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-source-names VAR_SOURCE_NAMES]
[--var-measurement-type VAR_MEASUREMENT_TYPE]
[--var-lib-kit VAR_LIB_KIT] [--var-batch VAR_BATCH]
[--var--lib-kit-cat-ids VAR__LIB_KIT_CAT_IDS]
[--var-instrument VAR_INSTRUMENT]
[--var-sample-type VAR_SAMPLE_TYPE]
[--var---assay-name VAR___ASSAY_NAME]
[--var---measurement-abbreviation VAR___MEASUREMENT_ABBREVIATION]
[--var---lib-strategy VAR___LIB_STRATEGY]
[--var---lib-selection VAR___LIB_SELECTION]
[--var-lib-layout VAR_LIB_LAYOUT]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-source-names
template variables ‚source_names‘
- --var-measurement-type
template variables ‚measurement_type‘
- --var-lib-kit
template variables ‚lib_kit‘
- --var-batch
template variables ‚batch‘
- --var--lib-kit-cat-ids
template variables ‚_lib_kit_cat_ids‘
- --var-instrument
template variables ‚instrument‘
- --var-sample-type
template variables ‚sample_type‘
- --var---assay-name
template variables ‚__assay_name‘
- --var---measurement-abbreviation
template variables ‚__measurement_abbreviation‘
- --var---lib-strategy
template variables ‚__lib_strategy‘
- --var---lib-selection
template variables ‚__lib_selection‘
- --var-lib-layout
template variables ‚lib_layout‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
mass_cytometry
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl mass_cytometry [-h] [--verbose]
[--var-investigation-identifier VAR_INVESTIGATION_IDENTIFIER]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-investigation-description VAR_INVESTIGATION_DESCRIPTION]
[--var-source-names VAR_SOURCE_NAMES]
[--var-organism VAR_ORGANISM]
[--var--organism-taxon VAR__ORGANISM_TAXON]
[--var-material VAR_MATERIAL]
[--var--material-ncit VAR__MATERIAL_NCIT]
[--var-tissue VAR_TISSUE]
[--var--tissue-ncit VAR__TISSUE_NCIT]
[--var-source-characteristics VAR_SOURCE_CHARACTERISTICS]
[--var-sample-suffixes VAR_SAMPLE_SUFFIXES]
[--var-sample-characteristics VAR_SAMPLE_CHARACTERISTICS]
[--var-sample-factors VAR_SAMPLE_FACTORS]
[--var-sample-factor-types VAR_SAMPLE_FACTOR_TYPES]
[--var-dissociation-type VAR_DISSOCIATION_TYPE]
[--var-sample-multiplexing VAR_SAMPLE_MULTIPLEXING]
[--var---s-file-name VAR___S_FILE_NAME]
[--var---assay-prefix VAR___ASSAY_PREFIX]
[--var---output-dir VAR___OUTPUT_DIR]
[--var---prompts-- VAR___PROMPTS__]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-identifier
template variables ‚investigation_identifier‘
- --var-investigation-title
template variables ‚investigation_title‘
- --var-investigation-description
template variables ‚investigation_description‘
- --var-source-names
template variables ‚source_names‘
- --var-organism
template variables ‚organism‘
- --var--organism-taxon
template variables ‚_organism_taxon‘
- --var-material
template variables ‚material‘
- --var--material-ncit
template variables ‚_material_ncit‘
- --var-tissue
template variables ‚tissue‘
- --var--tissue-ncit
template variables ‚_tissue_ncit‘
- --var-source-characteristics
template variables ‚source_characteristics‘
- --var-sample-suffixes
template variables ‚sample_suffixes‘
- --var-sample-characteristics
template variables ‚sample_characteristics‘
- --var-sample-factors
template variables ‚sample_factors‘
- --var-sample-factor-types
template variables ‚sample_factor_types‘
- --var-dissociation-type
template variables ‚dissociation_type‘
- --var-sample-multiplexing
template variables ‚sample_multiplexing‘
- --var---s-file-name
template variables ‚__s_file_name‘
- --var---assay-prefix
template variables ‚__assay_prefix‘
- --var---output-dir
template variables ‚__output_dir‘
- --var---prompts--
template variables ‚__prompts__‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
microarray
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl microarray [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-organism VAR_ORGANISM]
[--var--organisms VAR__ORGANISMS]
[--var-technology-platform VAR_TECHNOLOGY_PLATFORM]
[--var-array-design-ref VAR_ARRAY_DESIGN_REF]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-assay-name VAR_ASSAY_NAME]
[--var--terms VAR__TERMS]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-sample-names
template variables ‚sample_names‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var-organism
template variables ‚organism‘
- --var--organisms
template variables ‚_organisms‘
- --var-technology-platform
template variables ‚technology_platform‘
- --var-array-design-ref
template variables ‚array_design_ref‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var-assay-name
template variables ‚assay_name‘
- --var--terms
template variables ‚_terms‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
ms_meta_biocrates
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl ms_meta_biocrates [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-study-title VAR_STUDY_TITLE]
[--var-study-id VAR_STUDY_ID]
[--var-study-file-name VAR_STUDY_FILE_NAME]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-organism VAR_ORGANISM]
[--var--organisms VAR__ORGANISMS]
[--var-assay-measurement-type VAR_ASSAY_MEASUREMENT_TYPE]
[--var-assay-technology-type VAR_ASSAY_TECHNOLOGY_TYPE]
[--var--technology-types VAR__TECHNOLOGY_TYPES]
[--var-biocrates-kit VAR_BIOCRATES_KIT]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-assay-name VAR_ASSAY_NAME]
[--var-assay-measurement-abbreviation-LC VAR_ASSAY_MEASUREMENT_ABBREVIATION_LC]
[--var-assay-measurement-abbreviation-FIA VAR_ASSAY_MEASUREMENT_ABBREVIATION_FIA]
[--var-biocrates-metidq-version VAR_BIOCRATES_METIDQ_VERSION]
[--var-metaquac-version VAR_METAQUAC_VERSION]
[--var-instrument VAR_INSTRUMENT]
[--var--instruments VAR__INSTRUMENTS]
[--var-chromatography-instrument VAR_CHROMATOGRAPHY_INSTRUMENT]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-study-title
template variables ‚study_title‘
- --var-study-id
template variables ‚study_id‘
- --var-study-file-name
template variables ‚study_file_name‘
- --var-sample-names
template variables ‚sample_names‘
- --var-organism
template variables ‚organism‘
- --var--organisms
template variables ‚_organisms‘
- --var-assay-measurement-type
template variables ‚assay_measurement_type‘
- --var-assay-technology-type
template variables ‚assay_technology_type‘
- --var--technology-types
template variables ‚_technology_types‘
- --var-biocrates-kit
template variables ‚biocrates_kit‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-assay-name
template variables ‚assay_name‘
- --var-assay-measurement-abbreviation-LC
template variables ‚assay_measurement_abbreviation_LC‘
- --var-assay-measurement-abbreviation-FIA
template variables ‚assay_measurement_abbreviation_FIA‘
- --var-biocrates-metidq-version
template variables ‚biocrates_metidq_version‘
- --var-metaquac-version
template variables ‚metaquac_version‘
- --var-instrument
template variables ‚instrument‘
- --var--instruments
template variables ‚_instruments‘
- --var-chromatography-instrument
template variables ‚chromatography_instrument‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
single_cell_rnaseq
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl single_cell_rnaseq [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-lib-kit VAR_LIB_KIT]
[--var-source-meta VAR_SOURCE_META]
[--var-sample-meta VAR_SAMPLE_META]
[--var-dissociation-meta VAR_DISSOCIATION_META]
[--var-library-construction-meta VAR_LIBRARY_CONSTRUCTION_META]
[--var-sequencing-meta VAR_SEQUENCING_META]
[--var--library-types VAR__LIBRARY_TYPES]
[--var-library-type VAR_LIBRARY_TYPE]
[--var-sample-multiplexing VAR_SAMPLE_MULTIPLEXING]
[--var-genotype-multiplexing VAR_GENOTYPE_MULTIPLEXING]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-assay-name VAR_ASSAY_NAME]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-sample-names
template variables ‚sample_names‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var-lib-kit
template variables ‚lib_kit‘
- --var-source-meta
template variables ‚source_meta‘
- --var-sample-meta
template variables ‚sample_meta‘
- --var-dissociation-meta
template variables ‚dissociation_meta‘
- --var-library-construction-meta
template variables ‚library_construction_meta‘
- --var-sequencing-meta
template variables ‚sequencing_meta‘
- --var--library-types
template variables ‚_library_types‘
- --var-library-type
template variables ‚library_type‘
- --var-sample-multiplexing
template variables ‚sample_multiplexing‘
- --var-genotype-multiplexing
template variables ‚genotype_multiplexing‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var-assay-name
template variables ‚assay_name‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
somatic
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl somatic [-h] [--verbose]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-study-title VAR_STUDY_TITLE]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-source-names VAR_SOURCE_NAMES]
[--var-neoplasm-type VAR_NEOPLASM_TYPE]
[--var--neoplasm-terms VAR__NEOPLASM_TERMS]
[--var-measurement-type VAR_MEASUREMENT_TYPE]
[--var-lib-kit VAR_LIB_KIT]
[--var--lib-kit-cat-ids VAR__LIB_KIT_CAT_IDS]
[--var-instrument VAR_INSTRUMENT]
[--var-is-triplet VAR_IS_TRIPLET]
[--var---assay-name VAR___ASSAY_NAME]
[--var---measurement-abbreviation VAR___MEASUREMENT_ABBREVIATION]
[--var---lib-strategy VAR___LIB_STRATEGY]
[--var---lib-selection VAR___LIB_SELECTION]
[--var-lib-layout VAR_LIB_LAYOUT]
[--var---prompts-- VAR___PROMPTS__]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-investigation-title
template variables ‚investigation_title‘
- --var-study-title
template variables ‚study_title‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-source-names
template variables ‚source_names‘
- --var-neoplasm-type
template variables ‚neoplasm_type‘
- --var--neoplasm-terms
template variables ‚_neoplasm_terms‘
- --var-measurement-type
template variables ‚measurement_type‘
- --var-lib-kit
template variables ‚lib_kit‘
- --var--lib-kit-cat-ids
template variables ‚_lib_kit_cat_ids‘
- --var-instrument
template variables ‚instrument‘
- --var-is-triplet
template variables ‚is_triplet‘
- --var---assay-name
template variables ‚__assay_name‘
- --var---measurement-abbreviation
template variables ‚__measurement_abbreviation‘
- --var---lib-strategy
template variables ‚__lib_strategy‘
- --var---lib-selection
template variables ‚__lib_selection‘
- --var-lib-layout
template variables ‚lib_layout‘
- --var---prompts--
template variables ‚__prompts__‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
stem_cell_core_bulk
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl stem_cell_core_bulk [-h] [--verbose] [--var-group VAR_GROUP]
[--var-study-title VAR_STUDY_TITLE]
[--var-sample-numbers VAR_SAMPLE_NUMBERS]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-source-type VAR_SOURCE_TYPE]
[--var-cellline VAR_CELLLINE]
[--var-cellculture-meta VAR_CELLCULTURE_META]
[--var-model-type VAR_MODEL_TYPE]
[--var-sample-meta VAR_SAMPLE_META]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-library-kit VAR_LIBRARY_KIT]
[--var-library-construction-meta VAR_LIBRARY_CONSTRUCTION_META]
[--var-sequencing-meta VAR_SEQUENCING_META]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-assay-name VAR_ASSAY_NAME]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-group
template variables ‚group‘
- --var-study-title
template variables ‚study_title‘
- --var-sample-numbers
template variables ‚sample_numbers‘
- --var-investigation-title
template variables ‚investigation_title‘
- --var-source-type
template variables ‚source_type‘
- --var-cellline
template variables ‚cellline‘
- --var-cellculture-meta
template variables ‚cellculture_meta‘
- --var-model-type
template variables ‚model_type‘
- --var-sample-meta
template variables ‚sample_meta‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var-library-kit
template variables ‚library_kit‘
- --var-library-construction-meta
template variables ‚library_construction_meta‘
- --var-sequencing-meta
template variables ‚sequencing_meta‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-assay-name
template variables ‚assay_name‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
stem_cell_core_sc
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl stem_cell_core_sc [-h] [--verbose] [--var-group VAR_GROUP]
[--var-study-title VAR_STUDY_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-source-type VAR_SOURCE_TYPE]
[--var-cellline VAR_CELLLINE]
[--var-cellculture-meta VAR_CELLCULTURE_META]
[--var-model-type VAR_MODEL_TYPE]
[--var-sample-meta VAR_SAMPLE_META]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-library-kit VAR_LIBRARY_KIT]
[--var-dissociation-meta VAR_DISSOCIATION_META]
[--var-library-construction-meta VAR_LIBRARY_CONSTRUCTION_META]
[--var-sequencing-meta VAR_SEQUENCING_META]
[--var--library-types VAR__LIBRARY_TYPES]
[--var-library-type VAR_LIBRARY_TYPE]
[--var-sample-multiplexing VAR_SAMPLE_MULTIPLEXING]
[--var-genotype-multiplexing VAR_GENOTYPE_MULTIPLEXING]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-assay-name VAR_ASSAY_NAME]
[--var---output-dir VAR___OUTPUT_DIR]
output_dir
Positional Arguments
- output_dir
Path to output directory
Named Arguments
- --var-group
template variables ‚group‘
- --var-study-title
template variables ‚study_title‘
- --var-sample-names
template variables ‚sample_names‘
- --var-investigation-title
template variables ‚investigation_title‘
- --var-source-type
template variables ‚source_type‘
- --var-cellline
template variables ‚cellline‘
- --var-cellculture-meta
template variables ‚cellculture_meta‘
- --var-model-type
template variables ‚model_type‘
- --var-sample-meta
template variables ‚sample_meta‘
- --var-a-measurement-type
template variables ‚a_measurement_type‘
- --var-a-technology-type
template variables ‚a_technology_type‘
- --var-library-kit
template variables ‚library_kit‘
- --var-dissociation-meta
template variables ‚dissociation_meta‘
- --var-library-construction-meta
template variables ‚library_construction_meta‘
- --var-sequencing-meta
template variables ‚sequencing_meta‘
- --var--library-types
template variables ‚_library_types‘
- --var-library-type
template variables ‚library_type‘
- --var-sample-multiplexing
template variables ‚sample_multiplexing‘
- --var-genotype-multiplexing
template variables ‚genotype_multiplexing‘
- --var-s-file-name
template variables ‚s_file_name‘
- --var-assay-prefix
template variables ‚assay_prefix‘
- --var-assay-name
template variables ‚assay_name‘
- --var---output-dir
template variables ‚__output_dir‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
isa-tab
ISA-tab tools besides templating.
cubi-tk isa-tab [-h] {add-ped,validate} ...
Positional Arguments
- isa_tab_cmd
Possible choices: add-ped, validate
Sub-commands
add-ped
Add records from PED file to ISA-tab
cubi-tk isa-tab add-ped [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--sample-name-normalization {snappy,none}] [--yes]
[--dry-run] [--no-show-diff]
[--show-diff-side-by-side] [--batch-no BATCH_NO]
[--library-type {WES,WGS,Panel_seq}]
[--library-layout {SINGLE,PAIRED}]
[--library-kit LIBRARY_KIT]
[--library-kit-catalogue-id LIBRARY_KIT_CATALOGUE_ID]
[--platform PLATFORM]
[--instrument-model INSTRUMENT_MODEL]
investigation.tsv pedigree.ped
Positional Arguments
- investigation.tsv
Path to ISA-tab investigation file.
- pedigree.ped
Path to PLINK PED file with records to add.
Named Arguments
- --sample-name-normalization
Possible choices: snappy, none
Normalize sample names, default: snappy, choices: snappy, none
Default:
'snappy'- --yes
Assume all answers are yes.
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --no-show-diff, -D
Don’t show change when creating/updating sample sheets.
Default:
True- --show-diff-side-by-side
Show diff side by side instead of unified.
Default:
False- --batch-no
Value to set as the batch number.
Default:
'.'- --library-type
Possible choices: WES, WGS, Panel_seq
The library type.
Default:
'WES'- --library-layout
Possible choices: SINGLE, PAIRED
The library layout.
Default:
'PAIRED'- --library-kit
The library kit used.
Default:
''- --library-kit-catalogue-id
The library kit catalogue ID.
Default:
''- --platform
The string to use for the platform
Default:
'ILLUMINA'- --instrument-model
The string to use for the instrument model
Default:
''
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
validate
Validate ISA-tab
cubi-tk isa-tab validate [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--show-duplicate-warnings]
investigation.tsv
Positional Arguments
- investigation.tsv
Path to ISA-tab investigation file.
Named Arguments
- --show-duplicate-warnings
Show duplicated warnings, i.e. with same message and same category (False by default)
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
snappy
Tools for supporting the SNAPPY pipeline.
cubi-tk snappy [-h]
{check-local,check-remote,itransfer-raw-data,itransfer-ngs-mapping,itransfer-variant-calling,itransfer-sv-calling,itransfer-step,pull-sheets,pull-all-data,pull-processed-data,pull-raw-data,varfish-upload}
...
Positional Arguments
- snappy_cmd
Possible choices: check-local, check-remote, itransfer-raw-data, itransfer-ngs-mapping, itransfer-variant-calling, itransfer-sv-calling, itransfer-step, pull-sheets, pull-all-data, pull-processed-data, pull-raw-data, varfish-upload
Sub-commands
check-local
Check consistency within local sample sheet and between local sheets and files
cubi-tk snappy check-local [-h] [--verbose] [--base-path BASE_PATH]
[--tsv-shortcut {germline,cancer}]
[project_uuids ...]
Positional Arguments
- project_uuids
UUID(s) from project(s) to check. Use all if not given.
Named Arguments
- --tsv-shortcut
Possible choices: germline, cancer
The shortcut TSV schema to use.
Default:
'germline'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
check-remote
Check consistency within remote sample sheet and files
cubi-tk snappy check-remote [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--base-path BASE_PATH]
[--tsv-shortcut {cancer,generic,germline}] [--md5]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- --tsv-shortcut
Possible choices: cancer, generic, germline
The shortcut TSV schema to use.
Default:
'germline'- --md5
Flag to indicate if local and remote MD5 files should be compared.
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
itransfer-raw-data
Transfer FASTQs into iRODS landing zone
cubi-tk snappy itransfer-raw-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K]
[--yes] [--select-lz] [--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
destination
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy itransfer commands
- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --remote-dir-pattern
Pattern to use for constructing remote pattern
Default:
'{library_name}/{step}/{date}'
itransfer-ngs-mapping
Transfer ngs_mapping results into iRODS landing zone
cubi-tk snappy itransfer-ngs-mapping [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}]
[-K] [--yes] [--select-lz]
[--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--mapper MAPPER]
destination
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Named Arguments
- --mapper
Name of the mapper to transfer for, defaults to bwa.
Default:
'bwa'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy itransfer commands
- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --remote-dir-pattern
Pattern to use for constructing remote pattern
Default:
'{library_name}/{step}/{date}'
itransfer-variant-calling
Transfer variant_calling results into iRODS landing zone
cubi-tk snappy itransfer-variant-calling [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}]
[-K] [--yes] [--select-lz]
[--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--mapper MAPPER] [--caller CALLER]
destination
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Named Arguments
- --mapper
Name of the mapper to transfer for, defaults to bwa.
Default:
'bwa'- --caller
Name of the variant caller to transfer for, defaults to gatk_hc
Default:
'gatk_hc'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy itransfer commands
- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --remote-dir-pattern
Pattern to use for constructing remote pattern
Default:
'{library_name}/{step}/{date}'
itransfer-sv-calling
Transfer sv_calling or sv_calling_targeted results into iRODS landing zone
cubi-tk snappy itransfer-sv-calling [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K]
[--yes] [--select-lz]
[--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--mapper MAPPER] [--caller CALLER]
destination
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Named Arguments
- --mapper
Name of the mapper to transfer for, defaults to bwa_mem2.
Default:
'bwa_mem2'- --caller
Name of the variant caller to transfer for. Defaults to all callers defined in config
Default:
'all-defined'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy itransfer commands
- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --remote-dir-pattern
Pattern to use for constructing remote pattern
Default:
'{library_name}/{step}/{date}'
itransfer-step
Transfer snappy step results into iRODS landing zone
cubi-tk snappy itransfer-step [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K]
[--yes] [--select-lz] [--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN] --step
STEP [--tool [TOOL ...]]
destination
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Named Arguments
- --step
Name of the snappy pipeline step (step name must be identical to step directory).Steps names are available from the snappy command snappy-start-step –help
- --tool
Name of the tool, for example bwa. Tools order in important:it must match the order used to generate filename prefix.For example, the variant annotation step requires the mapper, caller andthe annotator software. In that case, the snappy file prefix is:<mapper>.<caller>.<annotator>, so the command would be:–tool <mapper> <vcaller> <annotator>. Some steps add more information to theirprefix, for example ‚jannovar_somatic_vcf‘
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy itransfer commands
- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --remote-dir-pattern
Pattern to use for constructing remote pattern
Default:
'{library_name}/{step}/{date}'
pull-sheets
Pull SODAR sample sheets into biomedsheet
cubi-tk snappy pull-sheets [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--base-path BASE_PATH]
[--yes] [--dry-run] [--no-show-diff]
[--show-diff-side-by-side]
[--library-types [{WES,WGS,Panel_seq} ...]]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--tsv-shortcut {cancer,generic,germline}]
Named Arguments
- --yes
Assume all answers are yes.
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --no-show-diff, -D
Don’t show change when creating/updating sample sheets.
Default:
True- --show-diff-side-by-side
Show diff side by side instead of unified.
Default:
False- --library-types
Possible choices: WES, WGS, Panel_seq
Library type(s) to use passed like ‚–library-types WES Panel_seq‘, default is to use all.
Default:
[]- --first-batch
First batch to be included in local sample sheet. Defaults: 0.
Default:
0- --last-batch
Last batch to be included in local sample sheet. Not used by default.
- --tsv-shortcut
Possible choices: cancer, generic, germline
The shortcut TSV schema to use; default: ‚germline‘.
Default:
'germline'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
pull-all-data
Pull all data from SODAR to specified output directory
cubi-tk snappy pull-all-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH] [--overwrite]
[--samples SAMPLES]
[--output-directory OUTPUT_DIRECTORY] [--yes]
[--allow-missing] [--dry-run]
[--irsync-threads IRSYNC_THREADS]
project_uuid
Named Arguments
- --allow-missing
Allow missing data in assay
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --irsync-threads
Parameter -N to pass to irsync
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy pull data commands
- --overwrite
Allow overwriting of files
Default:
False- --samples
Optional list of samples to pull
- --output-directory
Output directory, where downloaded files will be stored.
- --yes
Assume all answers are yes.
Default:
False- project_uuid
UUID of project to download data for.
pull-processed-data
Pull processed data from SODAR to specified output directory
cubi-tk snappy pull-processed-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID]
[--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH] [--overwrite]
[--samples SAMPLES]
[--output-directory OUTPUT_DIRECTORY]
[--yes] [--sample-id] --file-type
{bam,vcf,txt,csv,log}
[--download-all-versions]
project_uuid
Named Arguments
- --sample-id
Flag to indicate if search should be based on sample identifier (e.g.‘P001‘) instead of library name (e.g. ‚P001-N1-DNA1-WGS1‘).
Default:
False- --file-type
Possible choices: bam, vcf, txt, csv, log
File extensions to be retrieved. Valid options: (‚bam‘, ‚vcf‘, ‚txt‘, ‚csv‘, ‚log‘)
- --download-all-versions
By default only the latest version of a file will be download. For instance, if a was uploaded two times, in ‚2022-01-31‘ and ‚2022-02-28‘, only the latest is downloaded. If this flag is present, both versions will be downloaded.
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy pull data commands
- --overwrite
Allow overwriting of files
Default:
False- --samples
Optional list of samples to pull
- --output-directory
Output directory, where downloaded files will be stored.
- --yes
Assume all answers are yes.
Default:
False- project_uuid
UUID of project to download data for.
pull-raw-data
Pull raw data from SODAR to SNAPPY dataset raw data directory
cubi-tk snappy pull-raw-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--base-path BASE_PATH]
[--tsv-shortcut {germline,generic,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH] [--overwrite]
[--samples SAMPLES]
[--output-directory OUTPUT_DIRECTORY] [--yes]
[--dry-run] [--use-library-name]
project_uuid
Named Arguments
- --dry-run, -n
Perform a dry run, i.e., just displays the files that would be downloaded.
Default:
False- --use-library-name
Flag to indicate that the search in SODAR directories should be based on library name (e.g. ‚P001-N1-DNA1-WGS1‘) instead of sample identifier (e.g.‘P001‘) in the file name.
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Biomedsheet Configuration
- --tsv-shortcut
Possible choices: germline, generic, cancer
The shortcut TSV schema to use.
Default:
'germline'- --first-batch
First batch to be transferred. Defaults: 0.
Default:
0- --last-batch
Last batch to be transferred.
Configuration for snappy pull data commands
- --overwrite
Allow overwriting of files
Default:
False- --samples
Optional list of samples to pull
- --output-directory
Output directory, where downloaded files will be stored.
- --yes
Assume all answers are yes.
Default:
False- project_uuid
UUID of project to download data for.
varfish-upload
Upload variant analysis results into VarFish
cubi-tk snappy varfish-upload [-h] [--verbose] [--base-path BASE_PATH]
[--varfish-config VARFISH_CONFIG]
[--varfish-server-url VARFISH_SERVER_URL]
[--varfish-api-token VARFISH_API_TOKEN]
[--steps STEPS] [--external-data]
[--min-batch MIN_BATCH] [--yes]
[--force-resubmit] [--samples SAMPLES]
project [project ...]
Positional Arguments
- project
The UUID(s) of the SODAR project to submit.
Named Arguments
- --steps
Pipeline steps to consider for the export. Defaults to include all of the following; specify this with +name/-name to add/remove and either give multiple arguments or use a comma-separated list. {ngs_mapping, targeted_seq_cnv_export, varfish_export, variant_export, variant_export_external, wgs_cnv_export, wgs_cnv_export_external, wgs_sv_export, wgs_sv_export_external}
Default:
[]- --external-data
Flag to indicate that data was externally generated. Search for files will not filter based on common internally tool combinations, example: ‚bwa.delly2‘ or ‚bwa.gatk_hc‘.
Default:
False- --min-batch
Smallest batch to transfer, keep empty to transfer all.
- --yes, -y
Assume yes to all answers
Default:
False- --force-resubmit, -f
Force re-submission of exitsing cases in varfish.
Default:
False- --samples
Limits the submission to the listed sample names. Don’t include the full library name just the sample name (e.g., ‚P001‘ instead of ‚P001-N1-DNA1-WES1‘). Separate the sample with comma for multiple samples, example: ‚P001,P002,P003‘.
Default:
''
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Snappy Configuration
- --base-path
Base path of project (contains ‚.snappy_pipeline/‘ etc.), spiders up from current work directory and falls back to current working directory by default.
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
VarFish Configuration
- --varfish-config
Path to configuration file.
- --varfish-server-url
SODAR server URL key to use, defaults to env VARFISH_SERVER_URL.
- --varfish-api-token
SODAR API token to use, defaults to env VARFISH_API_TOKEN.
sodar
SODAR command line interface.
cubi-tk sodar [-h]
{add-ped,check-remote,download-sheet,deletion-requests,ingest-data,ingest-collection,pull-data,pull-raw-data,create-landingzone,list-landingzones,landing-zone-move,landing-zone-validate,update-samplesheet,upload-sheet}
...
Positional Arguments
- sodar_cmd
Possible choices: add-ped, check-remote, download-sheet, deletion-requests, ingest-data, ingest-collection, pull-data, pull-raw-data, create-landingzone, list-landingzones, landing-zone-move, landing-zone-validate, update-samplesheet, upload-sheet
Sub-commands
add-ped
Augment sample sheet from PED file
cubi-tk sodar add-ped [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN] [--dry-run]
[--show-diff] [--show-diff-side-by-side]
[--sample-name-normalization {snappy,none}] [--yes]
[--batch-no BATCH_NO]
[--library-type {WES,WGS,Panel_seq}]
[--library-layout {SINGLE,PAIRED}]
[--library-kit LIBRARY_KIT]
[--library-kit-catalogue-id LIBRARY_KIT_CATALOGUE_ID]
[--platform PLATFORM]
[--instrument-model INSTRUMENT_MODEL]
project_uuid pedigree.ped
Positional Arguments
- project_uuid
SODAR project UUID
- pedigree.ped
Path to PLINK PED file with records to add.
Named Arguments
- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --show-diff, -D
Show change when creating/updating sample sheets.
Default:
False- --show-diff-side-by-side
Show diff side by side instead of unified.
Default:
False- --sample-name-normalization
Possible choices: snappy, none
Normalize sample names, default: snappy, choices: snappy, none
Default:
'snappy'- --yes
Assume all answers are yes.
Default:
False- --batch-no
Value to set as the batch number.
Default:
'.'- --library-type
Possible choices: WES, WGS, Panel_seq
The library type.
Default:
'WES'- --library-layout
Possible choices: SINGLE, PAIRED
The library layout.
Default:
'PAIRED'- --library-kit
The library kit used.
Default:
''- --library-kit-catalogue-id
The library kit catalogue ID.
Default:
''- --platform
The string to use for the platform
Default:
'ILLUMINA'- --instrument-model
The string to use for the instrument model
Default:
''
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
check-remote
Compare local files with checksum against SODAR/iRODS
cubi-tk sodar check-remote [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [-p BASE_PATH]
[--filename-only] [--recheck-checksum]
[--report-checksums]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- -p, --base-path
Base path in which local files with checksums should be identified. Default: CWD
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'- --filename-only
Flag to indicate whether file comparison between local and remote files should only use file names and ignore checksum values.
Default:
False- --recheck-checksum
Flag to double check that checksums stored in local files do actually match their corresponding files
Default:
False- --report-checksums
Flag to indicate if checksums should be included in file report
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
download-sheet
Download ISA-tab
cubi-tk sodar download-sheet [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--no-makedirs] [--overwrite] [--yes] [--dry-run]
[--show-diff] [--show-diff-side-by-side]
project_uuid output_dir
Positional Arguments
- project_uuid
SODAR project UUID
- output_dir
Path to output directory to write the sheet to.
Named Arguments
- --no-makedirs
Create output directories
Default:
True- --overwrite
Allow overwriting of files
Default:
False- --yes
Assume all answers are yes.
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --show-diff, -D
Show change when creating/updating sample sheets.
Default:
False- --show-diff-side-by-side
Show diff side by side instead of unified.
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
deletion-requests
Create deletion reuqests for SODAR/iRODS
cubi-tk sodar deletion-requests [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID]
[-c COLLECTIONS [COLLECTIONS ...]]
[-d DESCRIPTION] [--dry-run]
project_uuid irods_paths [irods_paths ...]
Positional Arguments
- project_uuid
SODAR project UUID
- irods_paths
Paths to files or collections in irods that should get a deletion request. Relative paths will be taken in relation to the assay base path. Non-recursive wildcards (?/*) can be used, if literal strings are given.
Named Arguments
- -c, --collections
White list of base collections (samples), all files not matching these will not get a deletion request.
- -d, --description
Text description to be added to the deletion requests
- --dry-run, -n
Perform a dry run.
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
ingest-data
Upload files to SODAR project
cubi-tk sodar ingest-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K] [--yes]
[--select-lz] [--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[--preset {fastq,digestiflow,ONT,onk_analysis}]
[--src-regex SRC_REGEX]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--match-column MATCH_COLUMN] [-m MATCH REPL]
[--remote-dir-date REMOTE_DIR_DATE]
[--collection-column COLLECTION_COLUMN] [--tmp TMP]
destination sources [sources ...]
Positional Arguments
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
- sources
paths to folders
Named Arguments
- --preset
Possible choices: fastq, digestiflow, ONT, onk_analysis
Use predefined values for regular expression to find local files (–src-regex) and pattern to for constructing remote file paths. Default src-regex: (.*/)?(?P<sample>.+?)(?:_S[0-9]+)?(?:_(?P<lane>L[0-9]+?))?(?:_(?P<mate>R[0-9]+?))?(?:_(?P<batch>[0-9]+?))?.f(?:ast)?q.gz. Default –remote-dir-pattern: {collection_name}/raw_data/{date}/{filename}.
Default:
'fastq'- --src-regex
Manually defined regular expression to use for matching input files. Takes precedence over –preset. This regex controls which files are ingested, so it can be used for any file type. Any named capture group in the regex can be used with –remote-dir-pattern. The ‚sample‘ group is used to set irods collection names (as-is or via –match-column).
- --remote-dir-pattern
Manually defined pattern to use for constructing remote file paths. Takes precedence over –preset. ‚collection_name‘ is the target iRODS collection and will be filled with the (-m regex modified) ‚sample‘, or if –match-column is used with the corresponding value from the assay table. Any capture group of the src-regex (‚sample‘, ‚lane‘, …) can be used along with ‚date‘ and ‚filename‘.
- --match-column
Alternative assay column against which the {sample} from the src-regex should be matched, in order to determine collections based on the assay table (e.g. last material or collection-column). If not set it is assumed that {sample} matches the iRODS collections directly. If it matches multiple columns the last one can be used.
- -m, --sample-collection-mapping
Substitutions applied to the extracted sample name, which is used to determine iRODS collections.Can be used to change extracted string to correct collections names or to match the values of ‚–match-column‘.Use pythons regex syntax of ‚re.sub‘ package. This argument can be used multiple times (i.e. ‚-m <regex1> <repl1> -m <regex2> <repl2>‘ …).
Default:
[]- --remote-dir-date
Date to use in remote directory, defaults to YYYY-MM-DD of today.
Default:
'2025-09-24'- --collection-column
Assay column from that matches iRODS collection names. If not set, the last material column will be used. If it matches multiple columns the last one can be used.
- --tmp
Folder to save files from WebDAV temporarily, if set as source.
Default:
'temp/'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
ingest-collection
Upload a set of arbitrary files to a single iRODS colelction from SODAR
cubi-tk sodar ingest-collection [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K]
[--yes] [--select-lz] [--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
[-r] [-e EXCLUDE [EXCLUDE ...]]
[--collection COLLECTION]
sources [sources ...] destination
Positional Arguments
- sources
One or multiple files/directories to ingest.
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Named Arguments
- -r, --recursive
Recursively match files in subdirectories. Creates iRODS sub-collections to match directory structure.
Default:
False- -e, --exclude
Exclude files by defining one or multiple glob-style patterns.
Default:
''- --collection
Target iRODS collection. Skips manual target collection selection.
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
pull-data
Download data from iRODS
cubi-tk sodar pull-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--overwrite]
(-p {dragen} | -f FILE_PATTERN [FILE_PATTERN ...] | -a)
[--substring-match] [-s SAMPLE_LIST [SAMPLE_LIST ...]]
[--biomedsheet BIOMEDSHEET] [--tsv TSV]
[--tsv-column TSV_COLUMN]
[--tsv-skip-rows TSV_SKIP_ROWS] [-o OUTPUT_DIR]
[--output-pattern OUTPUT_PATTERN]
[--output-regex FILEPART MATCH REPL]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- --overwrite
Allow overwriting of local files.
Default:
False- -p, --preset
Possible choices: dragen
Preset to use for file selection.
- -f, --file-pattern
File pattern to use for file selection.
- -a, --all-files
Do not filter files, download everything.
Default:
False- -o, --output-dir
Output directory. Default: $PWD
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'- --output-pattern
Pattern for output files. Default: ‚{collection}/{subcollections}/{filename}‘
Default:
'{collection}/{subcollections}/{filename}'- --output-regex
Regular expression to change parts from iRODS path for output pattern. Syntax: ‚collection|subcollections|filename‘ ‚regex‘ ‚replacement’Can be given multiple times, Default: None
Default:
[]
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sample Filters
- --substring-match
Defined samples do not need to match collections exactly, a substring match is enough
Default:
False- -s, --sample-list
Sample list used for filtering collections.Takes precedence over –tsv and –biomedsheet.
- --biomedsheet
Biomedsheet file for filtering collections. Sets tsv-column to 2 and tsv-skip-rows to 12. Takes precedence over –tsv.
- --tsv
Tabular file with sample names to use for filtering collections.
- --tsv-column
Column index for sample entries in tsv file. Default: 1.
Default:
1- --tsv-skip-rows
Number of header lines in tsv file. Default: 0.
Default:
0
pull-raw-data
DEPRECATING! Download raw data from iRODS
cubi-tk sodar pull-raw-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--overwrite]
[--min-batch MIN_BATCH] [--allow-missing] [--yes]
[--dry-run] [--irsync-threads IRSYNC_THREADS]
project_uuid output_dir
Positional Arguments
- project_uuid
SODAR project UUID
- output_dir
Path to output directory to write the raw data to.
Named Arguments
- --overwrite
Allow overwriting of files
Default:
False- --min-batch
Minimal batch number to pull
Default:
0- --allow-missing
Allow missing data in assay
Default:
False- --yes
Assume all answers are yes.
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --irsync-threads
Parameter -N to pass to irsync
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
create-landingzone
Creating landing zone for project
cubi-tk sodar create-landingzone [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--unless-exists]
[--dry-run] [--format FORMAT_STRING]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- --unless-exists
If there already is a landing zone in the current project then use this one
Default:
False- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --format
Format string for printing, e.g. %(uuid)s
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
list-landingzones
List landing zones of project
cubi-tk sodar list-landingzones [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--dry-run] [--format FORMAT_STRING]
[--filter-status {ACTIVE,FAILED,VALIDATING}]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --format
Format string for printing, e.g. %(uuid)s
- --filter-status
Possible choices: ACTIVE, FAILED, VALIDATING
Filter landing zone by status. Defaults to listing all.
Default:
['ACTIVE', 'FAILED', 'VALIDATING']
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
landing-zone-move
Submit given landing zone for moving
cubi-tk sodar landing-zone-move [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--dry-run] [--format FORMAT_STRING]
landing_zone_uuid
Positional Arguments
- landing_zone_uuid
UUID of Landing Zone to move.
Named Arguments
- --dry-run, -n
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --format
Format string for printing, e.g. %(uuid)s
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
landing-zone-validate
Submit given landing zone for validation
cubi-tk sodar landing-zone-validate [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--format FORMAT_STRING]
landing_zone_uuid
Positional Arguments
- landing_zone_uuid
UUID of Landing Zone to move.
Named Arguments
- --format
Format string for printing, e.g. %(uuid)s
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
update-samplesheet
Update sample sheet
cubi-tk sodar update-samplesheet [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[-s SAMPLE_DATA [SAMPLE_DATA ...]]
[-d {ped_defaults,Modellvorhaben,MV,MV-barcodes,germline-sheet}]
[--sample-fields SAMPLE_FIELDS [SAMPLE_FIELDS ...]]
[-p PED]
[--ped-field-mapping PED_COLUMN SAMPLE_FIELD]
[--dynamic-column COLUMN FORMAT_STR]
[-a COLUMN VALUE] [--overwrite]
[--no-autofill] [--snappy-compatible]
project_uuid
Positional Arguments
- project_uuid
SODAR project UUID
Named Arguments
- -a, --metadata-all
Set metadata value for all samples added to the samplesheet. Specify column name and value. Can be used multiple times.
- --overwrite
Allow overwriting of existing values for samples already defined in the samplesheet
Default:
False- --no-autofill
Do not automatically fill values for non-specified metadata columns that have a single unique value in the existing samplesheet. Note: ontology terms & references will never be autofilled.
Default:
False- --snappy-compatible
Transform IDs so they are compatible with snappy processing (replaces ‚-‘ with ‚_‘ in required ISA fields).
Default:
False
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
Sample Definitions
- -s, --sample-data
Sample specific (meta)data to be added to the samplesheet. Each argument describes one sample. The number of arguments needs to match the fields defined via –defaults or –sample-fields`Can be combined with `–ped to give additional columns or additional samples. After joining both sets all fields must have a defined value.
- -d, --defaults
Possible choices: ped_defaults, Modellvorhaben, MV, MV-barcodes, germline-sheet
Modellvorhaben (10 fields, ped-Name: Analysis-ID): Family-ID, Analysis-ID, Paternal-ID, Maternal-ID, Sex, Phenotype, Individual-ID, Probe-ID, Barcode, Barcode-NameChoose a predefined default for field definitions (used by –sample-data) and –ped-name-mapping (used by –ped). Defaults to ‚germline-sheet‘. Field definitions are as follows:
MV (10 fields, ped-Name: Analysis-ID): Family-ID, Analysis-ID, Paternal-ID, Maternal-ID, Sex, Phenotype, Individual-ID, Probe-ID, Barcode, Barcode-NameChoose a predefined default for field definitions (used by –sample-data) and –ped-name-mapping (used by –ped). Defaults to ‚germline-sheet‘. Field definitions are as follows:
MV-barcodes (5 fields, ped-Name: Analysis-ID): Individual-ID, Probe-ID, Analysis-ID, Barcode, Barcode-NameChoose a predefined default for field definitions (used by –sample-data) and –ped-name-mapping (used by –ped). Defaults to ‚germline-sheet‘. Field definitions are as follows:
germline-sheet (6 fields, ped-Name: Sample-ID): Family-ID, Sample-ID, Paternal-ID, Maternal-ID, Sex, Phenotype
Default:
'germline-sheet'- --sample-fields
Manual definition of fields for –sample-data, overrides values set by –sheet-type. The field names need to match column names in the samplesheet, overrides –defaults.If values are given as ‚FieldName=ISAColumn‘, the Fields can be matched to ped columns, while also being matched to a differently named column in the ISA samplesheet.
- -p, --ped
Ped file with sample data to be added to the samplesheet, the default ped columns are mapped to these fields: Family-ID, Sample-ID(*), Paternal-ID, Maternal-ID, Sex, PhenoType. This mapping can be changed via –ped-field-mapping or the –defaults option. Can be extended by –sample-data to give additional columns or additional samples. After joining both sets all fields must have a defined value.
- --ped-field-mapping
family_idManually define how ped columns are mapped to sample data fields or ISA columns. The following ped names columns should be used: , nameManually define how ped columns are mapped to sample data fields or ISA columns. The following ped names columns should be used: , father_nameManually define how ped columns are mapped to sample data fields or ISA columns. The following ped names columns should be used: , mother_nameManually define how ped columns are mapped to sample data fields or ISA columns. The following ped names columns should be used: , sexManually define how ped columns are mapped to sample data fields or ISA columns. The following ped names columns should be used: , disease Overwrites value set for ‚name‘ by –defaults. SAMPLE_FIELD can also be a column name of the ISA samplesheet.
- --dynamic-column
Dynamically fill columns in the ISA sheet based on other columns.Use this option if some columns with sample-sepcific Data can be derived from other columns.FORMAT_STR can contain other columns as placeholders, i.e.: ‚{Source Name}-N1‘ for a new Sample Name.Note: only columns from the ped/sampledata can be used as placeholders.
upload-sheet
Upload and replace ISA-tab
cubi-tk sodar upload-sheet [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
project_uuid input_investigation_file
Positional Arguments
- project_uuid
SODAR project UUID
- input_investigation_file
Path to input investigation file.
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
sea-snap
Tools for supporting the RNA-SeASnaP pipeline.
cubi-tk sea-snap [-h]
{itransfer-raw-data,itransfer-results,working-dir,write-sample-info,check-irods}
...
Positional Arguments
- sea_snap_cmd
Possible choices: itransfer-raw-data, itransfer-results, working-dir, write-sample-info, check-irods
Sub-commands
itransfer-raw-data
Transfer FASTQs into iRODS landing zone
cubi-tk sea-snap itransfer-raw-data [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
itransfer-results
Transfer mapping results into iRODS landing zone
cubi-tk sea-snap itransfer-results [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--assay-uuid ASSAY_UUID] [--dry-run]
[--overwrite {sync,always,never,ask}] [-K]
[--yes] [--select-lz] [--validate-and-move]
[--parallel-checksum-jobs PARALLEL_CHECKSUM_JOBS]
transfer_blueprint destination
Positional Arguments
- transfer_blueprint
Path to blueprint file to load. This file contains commands to sync files with iRODS. Blocks of commands separated by an empty line will be executed together in one thread.
- destination
Sodar project UUID, landing-zone (irods) path or UUID to upload to.
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
- --assay-uuid
UUID from Assay to check. Used to specify target while dealing with multi-assay projects.
Sodar upload options
- --dry-run
Perform a dry-run, i.e. no actual upload.
Default:
False- --overwrite
Possible choices: sync, always, never, ask
Determine when to overwrite exising remote files. Default (sync) is to only do so when file sizes don’t match. Alternatively, overwrite always, never or ask for individual files.
Default:
'sync'- -K, --remote-checksums
Trigger checksum computation on the iRODS side.
Default:
False- --yes
Assume all answers are yes, e.g., will create or use existing available landing zones without asking.
Default:
False- --select-lz
Ask which available Landing zone to use. Note: –yes overrides this option.
Default:
False- --validate-and-move
After files are transferred to SODAR, it will proceed with validation and move.
Default:
False- --parallel-checksum-jobs
Number of threas to use for checksum calculation.
Default:
8
working-dir
Create working directory
cubi-tk sea-snap working-dir [-h] [--verbose] [--dry-run] [--dirname DIRNAME]
[--configs {mapping,DE} [{mapping,DE} ...]]
[sea_snap_path]
Positional Arguments
- sea_snap_path
Path into RNA-SeA-SnaP directory (below a directory containing ‚mapping_pipeline.snake‘).
Default:
'/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/stable'
Named Arguments
- --dry-run, -n
Perform dry-run, do not do anything.
Default:
False- --dirname, -d
Name of the working directory to create (default: ‚results_YEAR_MONTH_DAY/‘).
Default:
'results_%Y_%m_%d/'- --configs, -c
Possible choices: mapping, DE
Configs to be imported (default: all).
Default:
['mapping', 'DE']
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
write-sample-info
Generate sample info file
cubi-tk sea-snap write-sample-info [-h] [--verbose] [--config CONFIG]
[--config-profile CONFIG_PROFILE]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--allow-overwrite] [--dry-run]
[--show-diff] [--show-diff-side-by-side]
[--from-file FROM_FILE]
[--isa-assay ISA_ASSAY]
[--project_uuid PROJECT_UUID]
[--output_folder OUTPUT_FOLDER]
[--overwrite-isa]
in_path_pattern [output_file]
Positional Arguments
- in_path_pattern
Path pattern to use for extracting input file information. See https://cubi-gitlab.bihealth.org/CUBI/Pipelines/sea-snap/blob/master/documentation/prepare_input.md#fastq-files-folder-structure.
- output_file
Filename ending with ‚.yaml‘ or ‚.tsv‘. default: sample_info.yaml.
Default:
sample_info.yaml
Named Arguments
- --allow-overwrite
Allow to overwrite output file, default is not to allow overwriting output file.
Default:
False- --dry-run
Perform a dry run, i.e., don’t change anything only display change, implies ‚–show-diff‘.
Default:
False- --show-diff
Show change when creating/updating sample sheets.
Default:
False- --show-diff-side-by-side
Show diff side by side instead of unified.
Default:
False- --from-file
Path to yaml file to convert to tsv or tsv to yaml. Not used, if not specified.
- --isa-assay
Path to ISA assay file. Not used, if not specified.
Logging Configuration
- --verbose
Increase verbosity.
Default:
False
Basic Sodar Configuration
- --config
Path to configuration file.
Default:
'~/.cubitkrc.toml'- --config-profile
Sodar profile from configuration file and irods_environment_{config-profile}.json that should be used. If not specified global and irods_environment.json will be used
Default:
'global'- --sodar-server-url
SODAR server URL key to use.
- --sodar-api-token
SODAR API token to use.
pull ISA files
- --project_uuid
If set pull ISA files from SODAR. UUID of project to pull from.
Default:
False- --output_folder
Output folder path to store ISA files.
Default:
'ISA_files/'- --overwrite-isa
Allow to overwrite output file, default is not to allow overwriting output file.
Default:
False
check-irods
DEPRECATING! Check consistency of sample info, blueprint and files on SODAR
cubi-tk sea-snap check-irods [-h] [--verbose] [--num-replicas NUM_REPLICAS]
[--num-parallel-tests NUM_PARALLEL_TESTS] [--yes]
[--transfer-blueprint TRANSFER_BLUEPRINT]
results_folder irods_path
Positional Arguments
- results_folder
Path to a Sea-snap results folder.
- irods_path
Path to an iRods collection.
Named Arguments
- --num-replicas
Minimum number of replicas, defaults to 2
Default:
2- --num-parallel-tests
Number of parallel tests, defaults to 8
Default:
8- --yes
Assume the answer to all prompts is ‚yes‘
Default:
False- --transfer-blueprint
Filename of blueprint file for export to SODAR (created e.g. with ‚./sea-snap sc l export‘). Assumed to be in the results folder. Default: ‚SODAR_export_blueprint.txt‘
Default:
'SODAR_export_blueprint.txt'
Logging Configuration
- --verbose
Increase verbosity.
Default:
False