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} ...
Positional Arguments¶
| cmd | Possible choices: isa-tpl, isa-tab, snappy, sodar, irods, org-raw, sea-snap |
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,tumor_normal_dna,tumor_normal_triplets,germline,generic,microarray,ms_meta_biocrates}
...
Positional Arguments¶
| tpl | Possible choices: single_cell_rnaseq, tumor_normal_dna, tumor_normal_triplets, germline, generic, microarray, ms_meta_biocrates |
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-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-i-dir-name VAR_I_DIR_NAME]
[--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-lib-strand-specificity VAR_LIB_STRAND_SPECIFICITY]
[--var-library-name-mRNA VAR_LIBRARY_NAME_MRNA]
[--var-library-name-sample-tag VAR_LIBRARY_NAME_SAMPLE_TAG]
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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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-lib-strand-specificity | |
| template variables ‘lib_strand_specificity’ | |
| --var-library-name-mRNA | |
| template variables ‘library_name_mRNA’ | |
| --var-library-name-sample-tag | |
| template variables ‘library_name_sample_tag’ | |
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-i-dir-name VAR_I_DIR_NAME]
[--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]
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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ | |
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-i-dir-name VAR_I_DIR_NAME]
[--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]
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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ | |
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-i-dir-name VAR_I_DIR_NAME]
[--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]
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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ | |
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-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-i-dir-name VAR_I_DIR_NAME]
[--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]
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-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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ | |
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-i-dir-name VAR_I_DIR_NAME]
[--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]
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-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ |
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-i-dir-name VAR_I_DIR_NAME]
[--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]
output_dir
Positional Arguments¶
| output_dir | Path to output directory |
Named Arguments¶
| --var-investigation-title | |
| template variables ‘investigation_title’ | |
| --var-i-dir-name | |
| template variables ‘i_dir_name’ | |
| --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’ | |
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,itransfer-raw-data,itransfer-ngs-mapping,itransfer-variant-calling,pull-sheets,pull-raw-data,varfish-upload,kickoff}
...
Positional Arguments¶
| snappy_cmd | Possible choices: check, itransfer-raw-data, itransfer-ngs-mapping, itransfer-variant-calling, pull-sheets, pull-raw-data, varfish-upload, kickoff |
Sub-commands:¶
check¶
Check consistency within sample sheet and between sheet and files
cubi-tk snappy check [-h] [--tsv-shortcut {germline,cancer}]
[--base-path BASE_PATH]
biomedsheet_tsv [biomedsheet_tsv ...]
Positional Arguments¶
| biomedsheet_tsv | |
| Path to biomedsheets TSV file to load. | |
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. |
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}]
[--start-batch START_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
biomedsheet_tsv destination
Positional Arguments¶
| biomedsheet_tsv | |
| Path to biomedsheets TSV file to load. | |
| 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 | |
| --tsv-shortcut | Possible choices: germline, cancer The shortcut TSV schema to use. Default: “germline” |
| --start-batch | Batch to start the transfer at, defaults to 0. Default: 0 |
| --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/stable/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2021-05-05” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/raw_data/{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 | |
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}]
[--start-batch START_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--mapper MAPPER]
biomedsheet_tsv destination
Positional Arguments¶
| biomedsheet_tsv | |
| Path to biomedsheets TSV file to load. | |
| 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 | |
| --tsv-shortcut | Possible choices: germline, cancer The shortcut TSV schema to use. Default: “germline” |
| --start-batch | Batch to start the transfer at, defaults to 0. Default: 0 |
| --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/stable/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2021-05-05” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/ngs_mapping/{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 | |
| --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}]
[--start-batch START_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
[--mapper MAPPER] [--caller CALLER]
biomedsheet_tsv destination
Positional Arguments¶
| biomedsheet_tsv | |
| Path to biomedsheets TSV file to load. | |
| 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 | |
| --tsv-shortcut | Possible choices: germline, cancer The shortcut TSV schema to use. Default: “germline” |
| --start-batch | Batch to start the transfer at, defaults to 0. Default: 0 |
| --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/stable/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2021-05-05” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/variant_calling/{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 | |
| --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” |
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]
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/stable/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. | |
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] [--overwrite]
[--min-batch MIN_BATCH] [--samples SAMPLES]
[--yes] [--dry-run]
[--irsync-threads IRSYNC_THREADS] [--assay ASSAY]
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/stable/docs_manual” |
| --overwrite | Allow overwriting of files Default: False |
| --min-batch | Minimal batch number to pull Default: 0 |
| --samples | Optional list of samples to pull |
| --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. |
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]
[--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/stable/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, variant_export, wgs_cnv_export, wgs_sv_export} Default: [] |
| --min-batch | Smallest batch to transfer, keep empty to transfer all. |
| --yes, -y | Assume yes to all answers Default: False |
| --samples | The samples to limit the submission for, if any 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}
...
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 |
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] [--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 |
| --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/stable/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2021-05-05” | |
| --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/” |
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] [--num-replicas NUM_REPLICAS]
[--num-parallel-tests NUM_PARALLEL_TESTS]
irods_path
Positional Arguments¶
| 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 | |
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}]
[--start-batch START_BATCH]
[--base-path BASE_PATH]
[--remote-dir-date REMOTE_DIR_DATE]
[--remote-dir-pattern REMOTE_DIR_PATTERN]
[--yes] [--validate-and-move]
biomedsheet_tsv destination
Positional Arguments¶
| biomedsheet_tsv | |
| Path to biomedsheets TSV file to load. | |
| 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 | |
| --tsv-shortcut | Possible choices: germline, cancer The shortcut TSV schema to use. Default: “germline” |
| --start-batch | Batch to start the transfer at, defaults to 0. Default: 0 |
| --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/stable/docs_manual” |
| --remote-dir-date | |
Date to use in remote directory, defaults to YYYY-MM-DD of today. Default: “2021-05-05” | |
| --remote-dir-pattern | |
Pattern to use for constructing remote pattern Default: “{library_name}/raw_data/{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 | |
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/stable/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” | |