Command Line Interface¶
usage: cubi-tk [-h] [--verbose] [--version] [--config CONFIG]
[--sodar-server-url SODAR_SERVER_URL]
[--sodar-api-token SODAR_API_TOKEN]
{isa-tpl,isa-tab,snappy,sodar,irods,org-raw,sea-snap,archive}
...
Positional Arguments¶
| cmd | Possible choices: isa-tpl, isa-tab, snappy, sodar, irods, org-raw, sea-snap, archive |
Named Arguments¶
| --verbose | Increase verbosity. Default: False |
| --version | show program’s version number and exit |
Basic Configuration¶
| --config | Path to configuration file. |
| --sodar-server-url | |
| SODAR server URL key to use, defaults to env SODAR_SERVER_URL. | |
| --sodar-api-token | |
| SODAR API token to use, defaults to env SODAR_API_TOKEN. | |
Sub-commands¶
isa-tpl¶
Create of ISA-tab directories from predefined templates.
cubi-tk isa-tpl [-h]
{single_cell_rnaseq,bulk_rnaseq,tumor_normal_dna,tumor_normal_triplets,germline,generic,microarray,ms_meta_biocrates,stem_cell_core_bulk,stem_cell_core_sc}
...
Positional Arguments¶
| tpl | Possible choices: single_cell_rnaseq, bulk_rnaseq, tumor_normal_dna, tumor_normal_triplets, germline, generic, microarray, ms_meta_biocrates, stem_cell_core_bulk, stem_cell_core_sc |
Sub-commands¶
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]
[--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’ | |
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]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-a-measurement-types VAR_A_MEASUREMENT_TYPES]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-a-technology-types VAR_A_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-a-measurement-types | |
| template variables ‘a_measurement_types’ | |
| --var-a-technology-type | |
| template variables ‘a_technology_type’ | |
| --var-a-technology-types | |
| template variables ‘a_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’ | |
tumor_normal_dna¶
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl tumor_normal_dna [-h]
[--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-lib-kits VAR_LIB_KITS]
[--var-instrument VAR_INSTRUMENT]
[--var-center-name VAR_CENTER_NAME]
[--var-center-contact VAR_CENTER_CONTACT]
[--var-study-title VAR_STUDY_TITLE]
[--var-is-triplet VAR_IS_TRIPLET]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--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-lib-kit | template variables ‘lib_kit’ |
| --var-lib-kits | template variables ‘lib_kits’ |
| --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-is-triplet | |
| template variables ‘is_triplet’ | |
| --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-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’ | |
tumor_normal_triplets¶
When specifying the –var-* argument, you can use JSON syntax. Failing to parse JSON will keep the string value.
cubi-tk isa-tpl tumor_normal_triplets [-h]
[--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-lib-kits VAR_LIB_KITS]
[--var-instrument VAR_INSTRUMENT]
[--var-center-name VAR_CENTER_NAME]
[--var-center-contact VAR_CENTER_CONTACT]
[--var-study-title VAR_STUDY_TITLE]
[--var-is-triplet VAR_IS_TRIPLET]
[--var-s-file-name VAR_S_FILE_NAME]
[--var-assay-prefix VAR_ASSAY_PREFIX]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--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-lib-kit | template variables ‘lib_kit’ |
| --var-lib-kits | template variables ‘lib_kits’ |
| --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-is-triplet | |
| template variables ‘is_triplet’ | |
| --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-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’ | |
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]
[--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-batch VAR_BATCH]
[--var-lib-kits VAR_LIB_KITS]
[--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-technology-type VAR_A_TECHNOLOGY_TYPE]
[--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-lib-kit | template variables ‘lib_kit’ |
| --var-batch | template variables ‘batch’ |
| --var-lib-kits | template variables ‘lib_kits’ |
| --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-technology-type | |
| template variables ‘a_technology_type’ | |
| --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’ | |
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]
[--var-investigation-title VAR_INVESTIGATION_TITLE]
[--var-sample-names VAR_SAMPLE_NAMES]
[--var-a-measurement-type VAR_A_MEASUREMENT_TYPE]
[--var-a-measurement-types VAR_A_MEASUREMENT_TYPES]
[--var-a-technology-type VAR_A_TECHNOLOGY_TYPE]
[--var-a-technology-types VAR_A_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-a-measurement-types | |
| template variables ‘a_measurement_types’ | |
| --var-a-technology-type | |
| template variables ‘a_technology_type’ | |
| --var-a-technology-types | |
| template variables ‘a_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’ | |
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]
[--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’ | |
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]
[--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-assay-technology-types VAR_ASSAY_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-assay-technology-types | |
| template variables ‘assay_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’ | |
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] [--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’ | |
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] [--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’ | |
isa-tab¶
ISA-tab tools besides templating.
cubi-tk isa-tab [-h] {add-ped,resolve-hpo,annotate,validate} ...
Positional Arguments¶
| isa_tab_cmd | Possible choices: add-ped, resolve-hpo, annotate, validate |
Sub-commands¶
add-ped¶
Add records from PED file to ISA-tab
cubi-tk isa-tab add-ped [-h] [--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: “” | |
resolve-hpo¶
Resolve HPO term lists to ISA-tab fragments
cubi-tk isa-tab resolve-hpo [-h] [--hpo-obo-url HPO_OBO_URL] [term_file]
Positional Arguments¶
| term_file | Path to ISA-tab investigation file. Default: <_io.TextIOWrapper name=’<stdin>’ mode=’r’ encoding=’UTF-8’> |
Named Arguments¶
| --hpo-obo-url | Default URL to OBO file. Default: “http://purl.obolibrary.org/obo/hp.obo” |
annotate¶
Add annotation from CSV file to ISA-tab
cubi-tk isa-tab annotate [-h] [--yes] [--dry-run] [--no-show-diff]
[--show-diff-side-by-side] [--force-update]
[--target-study s_study.tsv]
[--target-assay a_assay.tsv]
investigation.tsv annotation.tsv
Positional Arguments¶
| investigation.tsv | |
| Path to ISA-tab investigation file. | |
| annotation.tsv | Path to annotation (TSV) file with information to add. |
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 | |
| --force-update | Overwrite non-empty ISA-tab entries. Default: False |
| --target-study, -s | |
| File name study to annotate. If not provided, first study in investigation is used. | |
| --target-assay, -a | |
| File name of assay to annotate. If not provided, first assay in investigation is used. | |
validate¶
Validate ISA-tab
cubi-tk isa-tab validate [-h] [--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 | |
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-step,pull-sheets,pull-all-data,pull-processed-data,pull-raw-data,varfish-upload,kickoff}
...
Positional Arguments¶
| snappy_cmd | Possible choices: check-local, check-remote, itransfer-raw-data, itransfer-ngs-mapping, itransfer-variant-calling, itransfer-step, pull-sheets, pull-all-data, pull-processed-data, pull-raw-data, varfish-upload, kickoff |
Sub-commands¶
check-local¶
Check consistency within local sample sheet and between local sheets and files
cubi-tk snappy check-local [-h] [--tsv-shortcut {germline,cancer}]
[--base-path BASE_PATH]
[project_uuids [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” |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), spiders up from biomedsheet_tsv and falls back to current working directory by default. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
check-remote¶
Check consistency within remote sample sheet and files
cubi-tk snappy check-remote [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--tsv-shortcut {cancer,generic,germline}]
[--base-path BASE_PATH] [--md5]
[--assay-uuid ASSAY_UUID]
project_uuid
Positional Arguments¶
| project_uuid | UUID from Project to check. |
Named Arguments¶
| --sodar-url | URL to SODAR, defaults to SODAR_URL environment variable or fallback to https://sodar.bihealth.org/ Default: “https://sodar.bihealth.org/” |
| --sodar-api-token | |
| Authentication token when talking to SODAR. Defaults to SODAR_API_TOKEN environment variable. | |
| --tsv-shortcut | Possible choices: cancer, generic, germline The shortcut TSV schema to use. Default: “germline” |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), spiders up from biomedsheet_tsv and falls back to current working directory by default. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --md5 | Flag to indicate if local and remote MD5 files should be compared. Default: False |
| --assay-uuid | UUID from Assay to check. Used to specify target while dealing with multi-assay projects. |
itransfer-raw-data¶
Transfer FASTQs into iRODS landing zone
cubi-tk snappy itransfer-raw-data [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--tsv-shortcut {germline,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--assay ASSAY]
destination
Positional Arguments¶
| destination | UUID from Landing Zone or Project - where files will be moved to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --tsv-shortcut | Possible choices: germline, 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. |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/{step}/{date}” | |
| --yes | Assume all answers are yes, e.g., will create or use existing available landing zones without asking. Default: False |
| --validate-and-move | |
After files are transferred to SODAR, it will proceed with validation and move. Default: False | |
| --assay | UUID of assay to download data for. |
itransfer-ngs-mapping¶
Transfer ngs_mapping results into iRODS landing zone
cubi-tk snappy itransfer-ngs-mapping [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--tsv-shortcut {germline,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--assay ASSAY] [--mapper MAPPER]
destination
Positional Arguments¶
| destination | UUID from Landing Zone or Project - where files will be moved to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --tsv-shortcut | Possible choices: germline, 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. |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/{step}/{date}” | |
| --yes | Assume all answers are yes, e.g., will create or use existing available landing zones without asking. Default: False |
| --validate-and-move | |
After files are transferred to SODAR, it will proceed with validation and move. Default: False | |
| --assay | UUID of assay to download data for. |
| --mapper | Name of the mapper to transfer for, defaults to bwa. Default: “bwa” |
itransfer-variant-calling¶
Transfer variant_calling results into iRODS landing zone
cubi-tk snappy itransfer-variant-calling [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--tsv-shortcut {germline,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--assay ASSAY] [--mapper MAPPER]
[--caller CALLER]
destination
Positional Arguments¶
| destination | UUID from Landing Zone or Project - where files will be moved to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --tsv-shortcut | Possible choices: germline, 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. |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/{step}/{date}” | |
| --yes | Assume all answers are yes, e.g., will create or use existing available landing zones without asking. Default: False |
| --validate-and-move | |
After files are transferred to SODAR, it will proceed with validation and move. Default: False | |
| --assay | UUID of assay to download data for. |
| --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” |
itransfer-step¶
Transfer snappy step results into iRODS landing zone
cubi-tk snappy itransfer-step [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--tsv-shortcut {germline,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move] [--assay ASSAY]
[--step STEP] [--tool [TOOL [TOOL ...]]]
destination
Positional Arguments¶
| destination | UUID from Landing Zone or Project - where files will be moved to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --tsv-shortcut | Possible choices: germline, 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. |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/{step}/{date}” | |
| --yes | Assume all answers are yes, e.g., will create or use existing available landing zones without asking. Default: False |
| --validate-and-move | |
After files are transferred to SODAR, it will proceed with validation and move. Default: False | |
| --assay | UUID of assay to download data for. |
| --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’ |
pull-sheets¶
Pull SODAR sample sheets into biomedsheet
cubi-tk snappy pull-sheets [-h] [--base-path BASE_PATH] [--yes] [--dry-run]
[--no-show-diff] [--show-diff-side-by-side]
[--library-types LIBRARY_TYPES]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--tsv-shortcut {cancer,generic,germline}]
Named Arguments¶
| --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/latest/docs_manual” |
| --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 | |
| Library type(s) to use, comma-separated, default is to use all. | |
| --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” |
pull-all-data¶
Pull all data from SODAR to specified output directory
cubi-tk snappy pull-all-data [-h] [--base-path BASE_PATH]
[--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
--output-directory OUTPUT_DIRECTORY [--overwrite]
[--first-batch FIRST_BATCH] [--samples SAMPLES]
[--allow-missing] [--yes] [--dry-run]
[--irsync-threads IRSYNC_THREADS]
[--assay ASSAY_UUID]
project_uuid
Positional Arguments¶
| project_uuid | UUID of project to download data for. |
Named Arguments¶
| --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/latest/docs_manual” |
| --output-directory | |
| Output directory, where downloaded files will be stored. | |
| --overwrite | Allow overwriting of files Default: False |
| --first-batch | First batch number to pull Default: 0 |
| --samples | Optional list of samples to pull |
| --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 | |
| --assay | UUID of assay to create landing zone for. |
pull-processed-data¶
Pull processed data from SODAR to specified output directory
cubi-tk snappy pull-processed-data [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--tsv-shortcut {cancer,generic,germline}]
[--base-path BASE_PATH]
[--selected-samples SELECTED_SAMPLES]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
--output-directory OUTPUT_DIRECTORY
[--sample-id] --file-type
{bam,vcf,txt,csv,log}
[--download-all-versions] [--overwrite]
[--assay-uuid ASSAY_UUID]
project_uuid
Positional Arguments¶
| project_uuid | UUID from Project to check. |
Named Arguments¶
| --sodar-url | URL to SODAR, defaults to SODAR_URL environment variable or fallback to https://sodar.bihealth.org/ Default: “https://sodar.bihealth.org/” |
| --sodar-api-token | |
| Authentication token when talking to SODAR. Defaults to SODAR_API_TOKEN environment variable. | |
| --tsv-shortcut | Possible choices: cancer, generic, germline The shortcut TSV schema to use; default: ‘germline’. Default: “germline” |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), spiders up from biomedsheet_tsv and falls back to current working directory by default. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --selected-samples | |
| Limits the request 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’. Note: argument overrides batch related arguments. | |
| --first-batch | First batch to be transferred. Defaults: 0. Default: 0 |
| --last-batch | Last batch to be transferred. |
| --output-directory | |
| Output directory, where downloaded files will be stored. | |
| --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 | |
| --overwrite | Allow overwriting of local files. Default: False |
| --assay-uuid | UUID from Assay to check. Used to specify target while dealing with multi-assay projects. |
pull-raw-data¶
Pull raw data from SODAR to SNAPPY dataset raw data directory
cubi-tk snappy pull-raw-data [-h] [--base-path BASE_PATH]
[--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN] [--dry-run]
[--overwrite]
[--tsv-shortcut {cancer,generic,germline}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH] [--samples SAMPLES]
[--use-library-name] [--assay-uuid ASSAY_UUID]
project_uuid
Positional Arguments¶
| project_uuid | UUID of project to download data for. |
Named Arguments¶
| --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/latest/docs_manual” |
| --dry-run, -n | Perform a dry run, i.e., just displays the files that would be downloaded. Default: False |
| --overwrite | Allow overwriting of files Default: False |
| --tsv-shortcut | Possible choices: cancer, generic, germline 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. |
| --samples | Optional list of samples to pull |
| --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 | |
| --assay-uuid | UUID of assay to create landing zone for. |
varfish-upload¶
Upload variant analysis results into VarFish
cubi-tk snappy varfish-upload [-h] [--varfish-config VARFISH_CONFIG]
[--varfish-server-url VARFISH_SERVER_URL]
[--varfish-api-token VARFISH_API_TOKEN]
[--base-path BASE_PATH] [--steps STEPS]
[--external-data] [--min-batch MIN_BATCH]
[--yes] [--samples SAMPLES]
project [project ...]
Positional Arguments¶
| project | The UUID(s) of the SODAR project to submit. |
Named Arguments¶
| --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/latest/docs_manual” |
| --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 |
| --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: “” |
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. | |
kickoff¶
Kick-off SNAPPY pipeline steps.
cubi-tk snappy kickoff [-h] [--dry-run] [--timeout TIMEOUT] [path]
Positional Arguments¶
| path | Path into SNAPPY directory (below a directory containing .snappy_pipeline). |
Named Arguments¶
| --dry-run, -n | Perform dry-run, do not do anything. Default: False |
| --timeout | Number of seconds to wait for commands. Default: 10 |
sodar¶
SODAR command line interface.
cubi-tk sodar [-h]
{add-ped,download-sheet,upload-sheet,pull-raw-data,landing-zone-create,landing-zone-list,landing-zone-move,ingest-fastq,check-remote}
...
Positional Arguments¶
| sodar_cmd | Possible choices: add-ped, download-sheet, upload-sheet, pull-raw-data, landing-zone-create, landing-zone-list, landing-zone-move, ingest-fastq, check-remote |
Sub-commands¶
add-ped¶
Augment sample sheet from PED file
cubi-tk sodar add-ped [-h] [--sodar-url SODAR_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 | UUID of project to download the ISA-tab for. |
| 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: “” | |
download-sheet¶
Download ISA-tab
cubi-tk sodar download-sheet [-h] [--sodar-url SODAR_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 | UUID of project to download the ISA-tab for. |
| 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 | |
upload-sheet¶
Upload and replace ISA-tab
cubi-tk sodar upload-sheet [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
project_uuid input_investigation_file
Positional Arguments¶
| project_uuid | UUID of project to upload the ISA-tab for. |
| input_investigation_file | |
| Path to input investigation file. | |
pull-raw-data¶
Download raw data from iRODS
cubi-tk sodar pull-raw-data [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN] [--overwrite]
[--min-batch MIN_BATCH] [--allow-missing] [--yes]
[--dry-run] [--irsync-threads IRSYNC_THREADS]
[--assay ASSAY]
project_uuid output_dir
Positional Arguments¶
| project_uuid | UUID of project to download data for. |
| 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 | |
| --assay | UUID of assay to download data for. |
landing-zone-create¶
Creating landing zone
cubi-tk sodar landing-zone-create [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--unless-exists] [--dry-run]
[--assay ASSAY] [--format FORMAT_STRING]
project_uuid
Positional Arguments¶
| project_uuid | UUID of project to create the landing zone in. |
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 |
| --assay | UUID of assay to create landing zone for. |
| --format | Format string for printing, e.g. %(uuid)s |
landing-zone-list¶
List landing zones
cubi-tk sodar landing-zone-list [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--unless-exists] [--dry-run]
[--format FORMAT_STRING]
project_uuid
Positional Arguments¶
| project_uuid | UUID of project to create the landing zone in. |
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 |
landing-zone-move¶
Submit landing zone for moving
cubi-tk sodar landing-zone-move [-h] [--sodar-url SODAR_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 |
ingest-fastq¶
Upload external files to SODAR (defaults for fastq)
cubi-tk sodar ingest-fastq [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--yes] [--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--src-regex SRC_REGEX]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--add-suffix ADD_SUFFIX] [-m MATCH REPL]
[--tmp TMP]
sources [sources ...] destination
Positional Arguments¶
| sources | paths to fastq folders |
| destination | UUID or iRods path of landing zone to move to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --yes | Assume the answer to all prompts is ‘yes’ Default: False |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --src-regex | Regular expression to use for matching input fastq files, default: (.*/)?(?P<sample>.+?)(?:_(?P<lane>L[0-9]+?))?(?:_(?P<mate>R[0-9]+?))?(?:_(?P<batch>[0-9]+?))?.f(?:ast)?q.gz Default: “(.*/)?(?P<sample>.+?)(?:_(?P<lane>L[0-9]+?))?(?:_(?P<mate>R[0-9]+?))?(?:_(?P<batch>[0-9]+?))?.f(?:ast)?q.gz” |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern, default: {sample}/{date}/{filename} Default: “{sample}/{date}/{filename}” | |
| --add-suffix | Suffix to add to all file names (e.g. ‘-N1-DNA1-WES1’). Default: “” |
| -m, --remote-dir-mapping | |
Substitutions applied to the filled remote dir paths. Can for example be used to modify sample names. Use pythons regex syntax of ‘re.sub’ package. This argument can be used multiple times (i.e. ‘-m <regex1> <repl1> -m <regex2> <repl2>’ …). Default: [] | |
| --tmp | Folder to save files from WebDAV temporarily, if set as source. Default: “temp/” |
check-remote¶
Compare local files with md5 sum against SODAR/iRODS
cubi-tk sodar check-remote [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN] [-p BASE_PATH]
[--filename-only] [--recheck-md5]
[--report-md5sums] [--assay-uuid ASSAY_UUID]
project_uuid
Positional Arguments¶
| project_uuid | UUID from Project to check. |
Named Arguments¶
| --sodar-url | URL to SODAR, defaults to SODAR_URL environment variable or fallback to https://sodar.bihealth.org/ Default: “https://sodar.bihealth.org/” |
| --sodar-api-token | |
| Authentication token when talking to SODAR. Defaults to SODAR_API_TOKEN environment variable. | |
| -p, --base-path | |
Base path in which local files with md5 sums should be identified. Default: CWD Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” | |
| --filename-only | |
Flag to indicate whether file comparison between local and remote files should only use file names and ignore md5 values. Default: False | |
| --recheck-md5 | Flag to double check that md5 sums stored in local files do actually match their corresponding files Default: False |
| --report-md5sums | |
Flag to indicate if md5 sums should be included in file report Default: False | |
| --assay-uuid | UUID from Assay to check. Used to specify target while dealing with multi-assay projects. |
irods¶
iRods command line interface.
cubi-tk irods [-h] {check} ...
Positional Arguments¶
| irods_cmd | Possible choices: check |
Sub-commands¶
check¶
Check target iRODS collection (all MD5 files? metadata MD5 consistent? enough replicas?).
cubi-tk irods check [-h] [-r REQ_NUM_REPS] [-p NUM_PARALLEL_TESTS]
[-d NUM_DISPLAY_FILES] [-s HASH_SCHEME]
irods_path
Positional Arguments¶
| irods_path | Path to an iRODS collection. |
Named Arguments¶
| -r, --num-replicas | |
Minimum number of replicas, defaults to 2 Default: 2 | |
| -p, --num-parallel-tests | |
Number of parallel tests, defaults to 4 Default: 4 | |
| -d, --num-display-files | |
Number of files listed when checking, defaults to 20 Default: 20 | |
| -s, --hash-scheme | |
Hash scheme used to verify checksums, defaults to MD5 Default: “MD5” | |
org-raw¶
org_raw command line interface.
cubi-tk org-raw [-h] {check,organize} ...
Positional Arguments¶
| org_raw_cmd | Possible choices: check, organize |
Sub-commands¶
check¶
Check consistency of raw data
cubi-tk org-raw check [-h] [--num-threads NUM_THREADS] [--no-gz-check]
[--no-md5-check] [--no-compute-md5]
[--missing-md5-error] [--create-md5-fail-no-error]
FILE.fastq.gz [FILE.fastq.gz ...]
Positional Arguments¶
| FILE.fastq.gz | Path(s) to .fastq.gz files to perform the check for |
Named Arguments¶
| --num-threads | Number of parallel threads Default: 0 |
| --no-gz-check | Deactivate check for gzip consistency (default is to perform check). Default: True |
| --no-md5-check | Deactivate comparison of MD5 sum if .md5 file exists (default is to perform check). Default: True |
| --no-compute-md5 | |
Deactivate computation of MD5 sum if missing (default is to compute MD5 sum). Default: True | |
| --missing-md5-error | |
Make missing .md5 files constitute an error. Default is to issue an log message only. Default: False | |
| --create-md5-fail-no-error | |
Make failure to create .md5 file not an error. Default is to make it an error. Default: True | |
organize¶
Check consistency of raw data
cubi-tk org-raw organize [-h] [--dry-run] [--yes] [--move] [--no-check]
[--src-regex SRC_REGEX] [--dest-pattern DEST_PATTERN]
[--num-threads NUM_THREADS] [--no-gz-check]
[--no-md5-check] [--no-compute-md5]
[--missing-md5-error] [--create-md5-fail-no-error]
out_path path.fastq.gz [path.fastq.gz ...]
Positional Arguments¶
| out_path | Path to output directory. |
| path.fastq.gz | Path to input files. |
Named Arguments¶
| --dry-run | Dry-run, do not actually do anything Default: False |
| --yes | Assume the answer to all prompts is ‘yes’ Default: False |
| --move | Move file(s) instead of copying, default is to copy. Default: False |
| --no-check | Do not run ‘raw-org check’ on output (default is to run). Default: True |
| --src-regex | Regular expression for parsing file paths. Default: (.*/)?(?P<sample>.+)(?:-.+?)?.f(?:ast)?q.gz Default: “(.*/)?(?P<sample>.+)(?:-.+?)?.f(?:ast)?q.gz” |
| --dest-pattern | Format expression for destination path generation. Default: {sample_name}/{file_name} Default: “{sample_name}/{file_name}” |
| --num-threads | Number of parallel threads Default: 0 |
| --no-gz-check | Deactivate check for gzip consistency (default is to perform check). Default: True |
| --no-md5-check | Deactivate comparison of MD5 sum if .md5 file exists (default is to perform check). Default: True |
| --no-compute-md5 | |
Deactivate computation of MD5 sum if missing (default is to compute MD5 sum). Default: True | |
| --missing-md5-error | |
Make missing .md5 files constitute an error. Default is to issue an log message only. Default: False | |
| --create-md5-fail-no-error | |
Make failure to create .md5 file not an error. Default is to make it an error. Default: True | |
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] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
[--tsv-shortcut {germline,cancer}]
[--first-batch FIRST_BATCH]
[--last-batch LAST_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--assay ASSAY]
destination
Positional Arguments¶
| destination | UUID from Landing Zone or Project - where files will be moved to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
| --tsv-shortcut | Possible choices: germline, 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. |
| --base-path | Base path of project (contains ‘ngs_mapping/’ etc.), defaults to current path. Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2023-07-04” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/{step}/{date}” | |
| --yes | Assume all answers are yes, e.g., will create or use existing available landing zones without asking. Default: False |
| --validate-and-move | |
After files are transferred to SODAR, it will proceed with validation and move. Default: False | |
| --assay | UUID of assay to download data for. |
itransfer-results¶
Transfer mapping results into iRODS landing zone
cubi-tk sea-snap itransfer-results [-h] [--sodar-url SODAR_URL]
[--sodar-api-token SODAR_API_TOKEN]
[--num-parallel-transfers NUM_PARALLEL_TRANSFERS]
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 | UUID or iRods path of landing zone to move to. |
Named Arguments¶
| --num-parallel-transfers | |
Number of parallel transfers, defaults to 8 Default: 8 | |
working-dir¶
Create working directory
cubi-tk sea-snap working-dir [-h] [--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/latest/docs_manual” |
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’] |
write-sample-info¶
Generate sample info file
cubi-tk sea-snap write-sample-info [-h] [--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] [--sodar-url SODAR_URL]
[--sodar-auth-token SODAR_AUTH_TOKEN]
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. |
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¶
Check consistency of sample info, blueprint and files on SODAR
cubi-tk sea-snap check-irods [-h] [--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” | |
archive¶
helper for archiving projects.
cubi-tk archive [-h] {copy,prepare,readme,summary} ...
Positional Arguments¶
| archive_cmd | Possible choices: copy, prepare, readme, summary |
Sub-commands¶
copy¶
Perform archival (copy and audit)
cubi-tk archive copy [-h] [--num-threads NUM_THREADS]
[--skip [SKIP [SKIP ...]]] [--keep-workdir-hashdeep]
[--read-only]
project destination
Positional Arguments¶
| project | Path of project directory |
| destination | Final destination directory for archive, must not exist |
Named Arguments¶
| --num-threads | Number of parallel threads Default: 4 |
| --skip | Step to skip (hashdeep, rsync, audit) |
| --keep-workdir-hashdeep | |
Save hashdeep report & audit of the temporary destination Default: False | |
| --read-only | Change destination files to read-only Default: False |
prepare¶
Prepare the project directory for archival
cubi-tk archive prepare [-h] [--num-threads NUM_THREADS] [--rules RULES]
[--readme README] [--ignore-tar-errors]
project destination
Positional Arguments¶
| project | Path of project directory |
| destination | Destination directory (for symlinks and later archival) |
Named Arguments¶
| --num-threads | Number of parallel threads Default: 4 |
| --rules, -r | Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/cubi_tk/archive/default_rules.yaml” |
| --readme | Path to README.md created with cubi-tk |
| --ignore-tar-errors | |
Ignore errors due to access permissions in when compressind folders Default: False | |
readme¶
Prepare a valid README.md
cubi-tk archive readme [-h] [--skip-collect] [--is-valid]
[--var-directory VAR_DIRECTORY]
[--var-PI-name VAR_PI_NAME]
[--var-PI-email VAR_PI_EMAIL]
[--var-archiver-name VAR_ARCHIVER_NAME]
[--var-archiver-email VAR_ARCHIVER_EMAIL]
[--var-CUBI-name VAR_CUBI_NAME]
[--var-client-name VAR_CLIENT_NAME]
[--var-client-email VAR_CLIENT_EMAIL]
[--var-SODAR-UUID VAR_SODAR_UUID]
[--var-SODAR-URL VAR_SODAR_URL]
[--var-Gitlab-URL VAR_GITLAB_URL]
[--var-project-name VAR_PROJECT_NAME]
[--var-start-date VAR_START_DATE]
[--var-current-status VAR_CURRENT_STATUS]
[--var-size VAR_SIZE] [--var-inodes VAR_INODES]
[--var-size-follow VAR_SIZE_FOLLOW]
[--var-inodes-follow VAR_INODES_FOLLOW]
[--var-snakemake-nb VAR_SNAKEMAKE_NB]
project filename
Positional Arguments¶
| project | Path of project directory |
| filename | README.md path & filename |
Named Arguments¶
| --skip-collect, -s | |
Skip the collection of file size & inodes Default: False | |
| --is-valid, -t | Test validity of existing README file Default: False |
| --var-directory | |
| template variable ‘directory’ | |
| --var-PI-name | template variable ‘PI_name’ |
| --var-PI-email | template variable ‘PI_email’ |
| --var-archiver-name | |
| template variable ‘archiver_name’ | |
| --var-archiver-email | |
| template variable ‘archiver_email’ | |
| --var-CUBI-name | |
| template variable ‘CUBI_name’ | |
| --var-client-name | |
| template variable ‘client_name’ | |
| --var-client-email | |
| template variable ‘client_email’ | |
| --var-SODAR-UUID | |
| template variable ‘SODAR_UUID’ | |
| --var-SODAR-URL | |
| template variable ‘SODAR_URL’ | |
| --var-Gitlab-URL | |
| template variable ‘Gitlab_URL’ | |
| --var-project-name | |
| template variable ‘project_name’ | |
| --var-start-date | |
| template variable ‘start_date’ | |
| --var-current-status | |
| template variable ‘current_status’ | |
| --var-size | template variable ‘size’ |
| --var-inodes | template variable ‘inodes’ |
| --var-size-follow | |
| template variable ‘size_follow’ | |
| --var-inodes-follow | |
| template variable ‘inodes_follow’ | |
| --var-snakemake-nb | |
| template variable ‘snakemake_nb’ | |
summary¶
Collects a summary of files in the project directory. The summary can be saved to a file for further inspection
cubi-tk archive summary [-h] [--classes CLASSES] [--dont-follow-links]
project table
Positional Arguments¶
| project | Path of project directory |
| table | Location of the summary output table |
Named Arguments¶
| --classes | Location of the file describing files of interest Default: “/home/docs/checkouts/readthedocs.org/user_builds/cubi-tk/checkouts/latest/cubi_tk/archive/classes.yaml” |
| --dont-follow-links | |
Do not follow symlinks to directories. Required when the project contains circular symlinks Default: False | |