# WfExS-backend stage definition - [1. Property `WfExS-backend stage definition > trs_endpoint`](#trs_endpoint) - [2. Property `WfExS-backend stage definition > version`](#version) - [3. Property `WfExS-backend stage definition > workflow_id`](#workflow_id) - [3.1. Property `WfExS-backend stage definition > workflow_id > anyOf > PlainURI`](#workflow_id_anyOf_i0) - [3.2. Property `WfExS-backend stage definition > workflow_id > anyOf > item 1`](#workflow_id_anyOf_i1) - [3.3. Property `WfExS-backend stage definition > workflow_id > anyOf > item 2`](#workflow_id_anyOf_i2) - [4. Property `WfExS-backend stage definition > nickname`](#nickname) - [5. Property `WfExS-backend stage definition > paranoid_mode`](#paranoid_mode) - [6. Property `WfExS-backend stage definition > workflow_type`](#workflow_type) - [7. Property `WfExS-backend stage definition > workflow_config`](#workflow_config) - [7.1. Property `WfExS-backend stage definition > workflow_config > secure`](#workflow_config_secure) - [7.2. Property `WfExS-backend stage definition > workflow_config > containerType`](#workflow_config_containerType) - [7.3. Property `WfExS-backend stage definition > workflow_config > writable_containers`](#workflow_config_writable_containers) - [7.4. Property `WfExS-backend stage definition > workflow_config > nextflow`](#workflow_config_nextflow) - [7.4.1. Property `WfExS-backend stage definition > workflow_config > nextflow > version`](#workflow_config_nextflow_version) - [7.4.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxRetries`](#workflow_config_nextflow_maxRetries) - [7.4.3. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses`](#workflow_config_nextflow_maxProcesses) - [7.4.3.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 0`](#workflow_config_nextflow_maxProcesses_oneOf_i0) - [7.4.3.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 1`](#workflow_config_nextflow_maxProcesses_oneOf_i1) - [7.4.4. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs`](#workflow_config_nextflow_maxCPUs) - [7.4.4.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 0`](#workflow_config_nextflow_maxCPUs_oneOf_i0) - [7.4.4.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 1`](#workflow_config_nextflow_maxCPUs_oneOf_i1) - [7.4.5. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration`](#workflow_config_nextflow_maxTaskDuration) - [7.4.5.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 0`](#workflow_config_nextflow_maxTaskDuration_oneOf_i0) - [7.4.5.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 1`](#workflow_config_nextflow_maxTaskDuration_oneOf_i1) - [7.4.6. Property `WfExS-backend stage definition > workflow_config > nextflow > profile`](#workflow_config_nextflow_profile) - [7.4.6.1. Property `WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 0`](#workflow_config_nextflow_profile_oneOf_i0) - [7.4.6.2. Property `WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1`](#workflow_config_nextflow_profile_oneOf_i1) - [7.4.6.2.1. WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1 > item 1 items](#autogenerated_heading_2) - [7.5. Property `WfExS-backend stage definition > workflow_config > cwl`](#workflow_config_cwl) - [7.5.1. Property `WfExS-backend stage definition > workflow_config > cwl > version`](#workflow_config_cwl_version) - [8. Property `WfExS-backend stage definition > placeholders`](#placeholders) - [8.1. Property `WfExS-backend stage definition > placeholders > additionalProperties`](#placeholders_additionalProperties) - [9. Property `WfExS-backend stage definition > params`](#params) - [9.1. Pattern Property `WfExS-backend stage definition > params > Param`](#params_pattern1) - [9.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 0`](#params_pattern1_pattern1_i0) - [9.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1`](#params_pattern1_pattern1_i1) - [9.1.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1 > item 1 items](#autogenerated_heading_3) - [9.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2`](#params_pattern1_pattern1_i2) - [9.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2 > item 2 items](#autogenerated_heading_4) - [9.1.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3`](#params_pattern1_pattern1_i3) - [9.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3 > item 3 items](#autogenerated_heading_5) - [9.1.5. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > DirFile`](#params_pattern1_pattern1_i4) - [9.1.5.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 0`](#params_pattern1_pattern1_i4_allOf_i0) - [9.1.5.1.1. If (c-l-a-s-s = Must be one of: * "Directory" * "File" )](#autogenerated_heading_6) - [9.1.5.1.1.1. Must **not** be](#autogenerated_heading_7) - [9.1.5.1.1.1.1. The following properties are required](#autogenerated_heading_8) - [9.1.5.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 1`](#params_pattern1_pattern1_i4_allOf_i1) - [9.1.5.2.1. If (c-l-a-s-s = "ContentWithURIs" )](#autogenerated_heading_9) - [9.1.5.2.1.1. Must **not** be](#autogenerated_heading_10) - [9.1.5.2.1.1.1. The following properties are required](#autogenerated_heading_11) - [9.1.5.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 2`](#params_pattern1_pattern1_i4_allOf_i2) - [9.1.5.3.1. If (c-l-a-s-s = Must be one of: * "Directory" * "File" )](#autogenerated_heading_12) - [9.1.5.3.1.1. Must **not** be](#autogenerated_heading_13) - [9.1.5.3.1.1.1. The following properties are required](#autogenerated_heading_14) - [9.1.5.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 3`](#params_pattern1_pattern1_i4_allOf_i3) - [9.1.5.4.1. If (c-l-a-s-s = "Directory" )](#autogenerated_heading_15) - [9.1.5.4.1.1. Must **not** be](#autogenerated_heading_16) - [9.1.5.4.1.1.1. The following properties are required](#autogenerated_heading_17) - [9.1.5.5. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 4`](#params_pattern1_pattern1_i4_allOf_i4) - [9.1.5.5.1. If (c-l-a-s-s = "File" )](#autogenerated_heading_18) - [9.1.5.5.1.1. Must **not** be](#autogenerated_heading_19) - [9.1.5.5.1.1.1. The following properties are required](#autogenerated_heading_20) - [9.1.5.6. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 5`](#params_pattern1_pattern1_i4_allOf_i5) - [9.1.5.6.1. If (c-l-a-s-s = "ContentWithURIs" )](#autogenerated_heading_21) - [9.1.5.6.1.1. Must **not** be](#autogenerated_heading_22) - [9.1.5.6.1.1.1. The following properties are required](#autogenerated_heading_23) - [9.1.5.7. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 6`](#params_pattern1_pattern1_i4_allOf_i6) - [9.1.5.7.1. If (c-l-a-s-s = "Value" )](#autogenerated_heading_24) - [9.1.5.7.1.1. Must **not** be](#autogenerated_heading_25) - [9.1.5.7.1.1.1. The following properties are required](#autogenerated_heading_26) - [9.1.5.7.1.2. The following properties are required](#autogenerated_heading_27) - [9.1.5.8. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 7`](#params_pattern1_pattern1_i4_allOf_i7) - [9.1.5.8.1. If (c-l-a-s-s = "ContentWithURIs" )](#autogenerated_heading_28) - [9.1.5.8.1.1. Must **not** be](#autogenerated_heading_29) - [9.1.5.8.1.1.1. The following properties are required](#autogenerated_heading_30) - [9.1.5.8.1.1.2. Must **not** be](#autogenerated_heading_31) - [9.1.5.8.1.1.2.1. The following properties are required](#autogenerated_heading_32) - [9.1.5.8.1.1.3. Must **not** be](#autogenerated_heading_33) - [9.1.5.8.1.1.3.1. The following properties are required](#autogenerated_heading_34) - [9.1.5.8.1.1.4. The following properties are required](#autogenerated_heading_35) - [9.1.5.8.1.2. The following properties are required](#autogenerated_heading_36) - [9.1.5.9. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > c-l-a-s-s`](#params_pattern1_pattern1_i4_c-l-a-s-s) - [9.1.5.10. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value`](#params_pattern1_pattern1_i4_value) - [9.1.5.10.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 0`](#params_pattern1_pattern1_i4_value_oneOf_i0) - [9.1.5.10.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1`](#params_pattern1_pattern1_i4_value_oneOf_i1) - [9.1.5.10.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1 > item 1 items](#autogenerated_heading_37) - [9.1.5.11. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular`](#params_pattern1_pattern1_i4_tabular) - [9.1.5.11.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns`](#params_pattern1_pattern1_i4_tabular_uri-columns) - [9.1.5.11.1.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns > uri-columns items](#autogenerated_heading_38) - [9.1.5.11.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > row-sep`](#params_pattern1_pattern1_i4_tabular_row-sep) - [9.1.5.11.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > column-sep`](#params_pattern1_pattern1_i4_tabular_column-sep) - [9.1.5.11.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > header-rows`](#params_pattern1_pattern1_i4_tabular_header-rows) - [9.1.5.12. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url`](#params_pattern1_pattern1_i4_url) - [9.1.5.12.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlainURI`](#params_pattern1_pattern1_i4_url_oneOf_i0) - [9.1.5.12.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlaceholderURI`](#params_pattern1_pattern1_i4_url_oneOf_i1) - [9.1.5.12.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > LicensedURI`](#params_pattern1_pattern1_i4_url_oneOf_i2) - [9.1.5.12.3.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri`](#params_pattern1_pattern1_i4_url_oneOf_i2_uri) - [9.1.5.12.3.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlainURI`](#params_pattern1_pattern1_i4_url_oneOf_i2_uri_anyOf_i0) - [9.1.5.12.3.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlaceholderURI`](#params_pattern1_pattern1_i4_url_oneOf_i2_uri_anyOf_i1) - [9.1.5.12.3.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences`](#params_pattern1_pattern1_i4_url_oneOf_i2_licences) - [9.1.5.12.3.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences > PlainURI](#autogenerated_heading_39) - [9.1.5.12.3.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions`](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions) - [9.1.5.12.3.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items](#autogenerated_heading_40) - [9.1.5.12.3.3.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > name`](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_name) - [9.1.5.12.3.3.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > pid`](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_pid) - [9.1.5.12.3.3.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles`](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_roles) - [9.1.5.12.3.3.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles > roles items](#autogenerated_heading_41) - [9.1.5.12.3.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > security-context`](#params_pattern1_pattern1_i4_url_oneOf_i2_security-context) - [9.1.5.12.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3`](#params_pattern1_pattern1_i4_url_oneOf_i3) - [9.1.5.12.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items](#autogenerated_heading_42) - [9.1.5.12.4.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > LicensedURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i0) - [9.1.5.12.4.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlainURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i1) - [9.1.5.12.4.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i2) - [9.1.5.12.4.1.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3) - [9.1.5.12.4.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items](#autogenerated_heading_43) - [9.1.5.12.4.1.4.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > LicensedURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i0) - [9.1.5.12.4.1.4.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlainURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i1) - [9.1.5.12.4.1.4.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI`](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i2) - [9.1.5.13. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > secondary-urls`](#params_pattern1_pattern1_i4_secondary-urls) - [9.1.5.14. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > preferred-name`](#params_pattern1_pattern1_i4_preferred-name) - [9.1.5.15. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > relative-dir`](#params_pattern1_pattern1_i4_relative-dir) - [9.1.5.16. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > security-context`](#params_pattern1_pattern1_i4_security-context) - [9.1.5.17. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > disclosable`](#params_pattern1_pattern1_i4_disclosable) - [9.1.5.18. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > cacheable`](#params_pattern1_pattern1_i4_cacheable) - [9.1.5.19. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > clonable`](#params_pattern1_pattern1_i4_clonable) - [9.1.5.20. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > globExplode`](#params_pattern1_pattern1_i4_globExplode) - [9.1.5.21. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoFill`](#params_pattern1_pattern1_i4_autoFill) - [9.1.5.22. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoPrefix`](#params_pattern1_pattern1_i4_autoPrefix) - [9.1.6. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > Params`](#params_pattern1_pattern1_i5) - [10. Property `WfExS-backend stage definition > profile`](#profile) - [10.1. Property `WfExS-backend stage definition > profile > oneOf > item 0`](#profile_oneOf_i0) - [10.2. Property `WfExS-backend stage definition > profile > oneOf > item 1`](#profile_oneOf_i1) - [10.2.1. WfExS-backend stage definition > profile > oneOf > item 1 > item 1 items](#autogenerated_heading_44) - [11. Property `WfExS-backend stage definition > environment`](#environment) - [11.1. Pattern Property `WfExS-backend stage definition > environment > EnvVar`](#environment_pattern1) - [11.1.1. Property `WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > item 0`](#environment_pattern1_pattern1_i0) - [11.1.2. Property `WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > DirFile`](#environment_pattern1_pattern1_i1) - [12. Property `WfExS-backend stage definition > outputs`](#outputs) - [12.1. Pattern Property `WfExS-backend stage definition > outputs > ^[^:;]+$`](#outputs_pattern1) - [12.1.1. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > c-l-a-s-s`](#outputs_pattern1_c-l-a-s-s) - [12.1.2. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality`](#outputs_pattern1_cardinality) - [12.1.2.1. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 0`](#outputs_pattern1_cardinality_oneOf_i0) - [12.1.2.2. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 1`](#outputs_pattern1_cardinality_oneOf_i1) - [12.1.2.3. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2`](#outputs_pattern1_cardinality_oneOf_i2) - [12.1.2.3.1. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 0](#autogenerated_heading_45) - [12.1.2.3.2. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 1](#autogenerated_heading_46) - [12.1.3. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > preferredName`](#outputs_pattern1_preferredName) - [12.1.4. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > fillFrom`](#outputs_pattern1_fillFrom) - [12.1.5. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > syntheticOutput`](#outputs_pattern1_syntheticOutput) - [12.1.6. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > glob`](#outputs_pattern1_glob) - [13. Property `WfExS-backend stage definition > default_actions`](#default_actions) **Title:** WfExS-backend stage definition | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | **Description:** WfExS-backend stage definition file (EOSC-Life Demonstrator 7 JSON Schemas) | Property | Pattern | Type | Deprecated | Definition | Title/Description | | -------------------------------------- | ------- | ----------------- | ---------- | ------------------------- | --------------------------------------------------------------------------------------------------- | | - [trs_endpoint](#trs_endpoint ) | No | string | No | In #/definitions/PlainURI | The optional TRS endpoing | | - [version](#version ) | No | string or integer | No | - | Workflow version | | + [workflow_id](#workflow_id ) | No | Combination | No | - | - | | - [nickname](#nickname ) | No | string | No | - | A friendly nickname (prefix) for the instances | | - [paranoid_mode](#paranoid_mode ) | No | boolean | No | - | - | | - [workflow_type](#workflow_type ) | No | string | No | - | The optional, forced workflow type | | - [workflow_config](#workflow_config ) | No | object | No | - | - | | - [placeholders](#placeholders ) | No | object | No | - | - | | - [params](#params ) | No | object | No | In #/definitions/Params | - | | - [profile](#profile ) | No | Combination | No | - | For engines which support profiles, like Nextflow or snakemake, if defined, the profile/s to enable | | - [environment](#environment ) | No | object | No | - | - | | - [outputs](#outputs ) | No | object | No | - | - | | - [default_actions](#default_actions ) | No | array | No | - | - | ## 1. Property `WfExS-backend stage definition > trs_endpoint` **Title:** The optional TRS endpoing | | | | -------------- | ---------------------- | | **Type** | `string` | | **Required** | No | | **Defined in** | #/definitions/PlainURI | **Description:** If this key is set, it will tell the GA4GH TRS service where to look for the workflow_id (and optional version) | Restrictions | | | -------------- | - | | **Min length** | 1 | ## 2. Property `WfExS-backend stage definition > version` **Title:** Workflow version | | | | ------------ | ------------------- | | **Type** | `string or integer` | | **Required** | No | **Description:** If trs_enpoint key is set, it will tell the version of the workflow_id to look for at GA4GH TRS ## 3. Property `WfExS-backend stage definition > workflow_id` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | Yes | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Any of(Option) | | --------------------------------- | | [PlainURI](#workflow_id_anyOf_i0) | | [item 1](#workflow_id_anyOf_i1) | | [item 2](#workflow_id_anyOf_i2) | ### 3.1. Property `WfExS-backend stage definition > workflow_id > anyOf > PlainURI` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [trs_endpoint](#trs_endpoint) | ### 3.2. Property `WfExS-backend stage definition > workflow_id > anyOf > item 1` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | ### 3.3. Property `WfExS-backend stage definition > workflow_id > anyOf > item 2` | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | ## 4. Property `WfExS-backend stage definition > nickname` **Title:** A friendly nickname (prefix) for the instances | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | ## 5. Property `WfExS-backend stage definition > paranoid_mode` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `false` | ## 6. Property `WfExS-backend stage definition > workflow_type` **Title:** The optional, forced workflow type | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** When this key is set, it is forcing the workflow type. WfExS-backend is usually able to identify the workflow type, unless there are two intertwined workflows in the same location ## 7. Property `WfExS-backend stage definition > workflow_config` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | -------------------------------------------------------------- | ------- | ---------------- | ---------- | ---------- | ------------------------------------------------------ | | - [secure](#workflow_config_secure ) | No | boolean | No | - | - | | - [containerType](#workflow_config_containerType ) | No | enum (of string) | No | - | Container technology type to be used for this workflow | | - [writable_containers](#workflow_config_writable_containers ) | No | boolean | No | - | - | | - [nextflow](#workflow_config_nextflow ) | No | object | No | - | - | | - [cwl](#workflow_config_cwl ) | No | object | No | - | - | ### 7.1. Property `WfExS-backend stage definition > workflow_config > secure` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | ### 7.2. Property `WfExS-backend stage definition > workflow_config > containerType` **Title:** Container technology type to be used for this workflow | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | No | **Description:** Type of container technology to be used when this staging scenario is instantiated. Supported types are: - Singularity (default). - Docker. - Podman - No containerisation technology (discouraged, but needed for some workflows) Encrypted working directories are unsupported when Docker or Podman are used due technological limitations Must be one of: * "singularity" * "docker" * "podman" * "none" ### 7.3. Property `WfExS-backend stage definition > workflow_config > writable_containers` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `false` | ### 7.4. Property `WfExS-backend stage definition > workflow_config > nextflow` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | --------------------------------------------------------------- | ------- | ----------- | ---------- | ---------- | ------------------------------------------------ | | - [version](#workflow_config_nextflow_version ) | No | string | No | - | - | | - [maxRetries](#workflow_config_nextflow_maxRetries ) | No | integer | No | - | Retries in docker mode | | - [maxProcesses](#workflow_config_nextflow_maxProcesses ) | No | Combination | No | - | (deprecated) Max number of CPUs | | - [maxCPUs](#workflow_config_nextflow_maxCPUs ) | No | Combination | No | - | (deprecated) Max number of CPUs | | - [maxTaskDuration](#workflow_config_nextflow_maxTaskDuration ) | No | Combination | No | - | Max task duration | | - [profile](#workflow_config_nextflow_profile ) | No | Combination | No | - | (deprecated) If defined, the profile/s to enable | #### 7.4.1. Property `WfExS-backend stage definition > workflow_config > nextflow > version` | | | | ------------ | ----------- | | **Type** | `string` | | **Required** | No | | **Default** | `"19.04.1"` | | Restrictions | | | -------------- | - | | **Min length** | 1 | #### 7.4.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxRetries` **Title:** Retries in docker mode | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | **Default** | `5` | **Description:** Retries when `engineMode` is `docker`. Retries system was introduced when using docker-in-docker pattern because an insidious bug happens sometimes. See https://forums.docker.com/t/any-known-problems-with-symlinks-on-bind-mounts/32138 | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 0 | #### 7.4.3. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses` **Title:** (deprecated) Max number of CPUs | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** Number of CPUs to be used by Nextflow. When this key has an explicit value of `null`, it depends on Nextflow criteria, which tries creating as many processes as available CPUs, spawning jobs in parallel. Not declaring it, or declaring and explicit value, imposes a limitation in the number of concurrent processes | One of(Option) | | --------------------------------------------------------- | | [item 0](#workflow_config_nextflow_maxProcesses_oneOf_i0) | | [item 1](#workflow_config_nextflow_maxProcesses_oneOf_i1) | ##### 7.4.3.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 0` | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | **Default** | `4` | | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 1 | ##### 7.4.3.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 1` | | | | ------------ | ------ | | **Type** | `null` | | **Required** | No | #### 7.4.4. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs` **Title:** (deprecated) Max number of CPUs | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** Number of CPUs to be used by Nextflow. When this key has an explicit value of `null`, it depends on Nextflow criteria, which tries creating as many processes as available CPUs, spawning jobs in parallel. Not declaring it, or declaring and explicit value, imposes a limitation in the number of concurrent processes | One of(Option) | | ---------------------------------------------------- | | [item 0](#workflow_config_nextflow_maxCPUs_oneOf_i0) | | [item 1](#workflow_config_nextflow_maxCPUs_oneOf_i1) | ##### 7.4.4.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 0` | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | **Default** | `4` | | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 1 | ##### 7.4.4.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 1` | | | | ------------ | ------ | | **Type** | `null` | | **Required** | No | #### 7.4.5. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration` **Title:** Max task duration | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** With this parameter it is possible to override the max task time declared for processes. This is needed for workflows which are not so customizable | One of(Option) | | ------------------------------------------------------------ | | [item 0](#workflow_config_nextflow_maxTaskDuration_oneOf_i0) | | [item 1](#workflow_config_nextflow_maxTaskDuration_oneOf_i1) | ##### 7.4.5.1. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 0` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | --------------------------------------------------------------------------- | | **Must match regular expression** | ```^[0-9]+.*$``` [Test](https://regex101.com/?regex=%5E%5B0-9%5D%2B.%2A%24) | ##### 7.4.5.2. Property `WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 1` | | | | ------------ | ------ | | **Type** | `null` | | **Required** | No | #### 7.4.6. Property `WfExS-backend stage definition > workflow_config > nextflow > profile` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** (deprecated) If defined, the profile/s to enable | One of(Option) | | ---------------------------------------------------- | | [item 0](#workflow_config_nextflow_profile_oneOf_i0) | | [item 1](#workflow_config_nextflow_profile_oneOf_i1) | ##### 7.4.6.1. Property `WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 0` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$``` [Test](https://regex101.com/?regex=%5E%5B%5E%2C+%09%5D%2B%5B+%09%5D%2A%28%2C%5B+%09%5D%2A%5B%5E%2C+%09%5D%2B%5B+%09%5D%2A%29%2A%24) | ##### 7.4.6.2. Property `WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1` | | | | ------------ | ----------------- | | **Type** | `array of string` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | ---------------------------------------------------------------- | ----------- | | [item 1 items](#workflow_config_nextflow_profile_oneOf_i1_items) | - | ###### 7.4.6.2.1. WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1 > item 1 items | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | ----------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```^[^,]+$``` [Test](https://regex101.com/?regex=%5E%5B%5E%2C%5D%2B%24) | ### 7.5. Property `WfExS-backend stage definition > workflow_config > cwl` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ------------------------------------------ | ------- | ------ | ---------- | ---------- | ----------------- | | - [version](#workflow_config_cwl_version ) | No | string | No | - | - | #### 7.5.1. Property `WfExS-backend stage definition > workflow_config > cwl > version` | | | | ------------ | ---------------------- | | **Type** | `string` | | **Required** | No | | **Default** | `"3.1.20210628163208"` | | Restrictions | | | -------------- | - | | **Min length** | 1 | ## 8. Property `WfExS-backend stage definition > placeholders` | | | | ------------------------- | ---------------------------------------------------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Should-conform]](#placeholders_additionalProperties "Each additional property must conform to the following schema") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ----------------------------------------- | ------- | ------------------------- | ---------- | ---------- | ----------------- | | - [](#placeholders_additionalProperties ) | No | number, integer or string | No | - | - | ### 8.1. Property `WfExS-backend stage definition > placeholders > additionalProperties` | | | | ------------ | --------------------------- | | **Type** | `number, integer or string` | | **Required** | No | ## 9. Property `WfExS-backend stage definition > params` | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Defined in** | #/definitions/Params | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | -------------------------------------------- | ------- | ------ | ---------- | ---------------------- | ----------------- | | - [^(?!c-l-a-s-s)[^:;]+$](#params_pattern1 ) | Yes | object | No | In #/definitions/Param | - | ### 9.1. Pattern Property `WfExS-backend stage definition > params > Param` > All properties whose name matches the regular expression ```^(?!c-l-a-s-s)[^:;]+$``` ([Test](https://regex101.com/?regex=%5E%28%3F%21c-l-a-s-s%29%5B%5E%3A%3B%5D%2B%24)) must respect the following conditions | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | **Defined in** | #/definitions/Param | | One of(Option) | | --------------------------------------- | | [item 0](#params_pattern1_pattern1_i0) | | [item 1](#params_pattern1_pattern1_i1) | | [item 2](#params_pattern1_pattern1_i2) | | [item 3](#params_pattern1_pattern1_i3) | | [DirFile](#params_pattern1_pattern1_i4) | | [Params](#params_pattern1_pattern1_i5) | #### 9.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 0` | | | | ------------ | --------------------------- | | **Type** | `string, number or boolean` | | **Required** | No | #### 9.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1` | | | | ------------ | ----------------- | | **Type** | `array of string` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | -------------------------------------------------- | ----------- | | [item 1 items](#params_pattern1_pattern1_i1_items) | - | ##### 9.1.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1 > item 1 items | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | #### 9.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2` | | | | ------------ | ----------------- | | **Type** | `array of number` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | -------------------------------------------------- | ----------- | | [item 2 items](#params_pattern1_pattern1_i2_items) | - | ##### 9.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2 > item 2 items | | | | ------------ | -------- | | **Type** | `number` | | **Required** | No | #### 9.1.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3` | | | | ------------ | ------------------ | | **Type** | `array of boolean` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | -------------------------------------------------- | ----------- | | [item 3 items](#params_pattern1_pattern1_i3_items) | - | ##### 9.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3 > item 3 items | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | #### 9.1.5. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > DirFile` | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Defined in** | #/definitions/DirFile | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | -------------------------------------------------------------------- | ------- | ----------------- | ---------- | ------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | + [c-l-a-s-s](#params_pattern1_pattern1_i4_c-l-a-s-s ) | No | enum (of string) | No | - | - | | - [value](#params_pattern1_pattern1_i4_value ) | No | Combination | No | - | When 'c-l-a-s-s' is a single file or a value, the assigned value | | - [tabular](#params_pattern1_pattern1_i4_tabular ) | No | object | No | - | When it is content with URIs, we are telling it is a tabular one with this key. URIs are fetched, and the absolute paths replace them in the generated content tab | | - [url](#params_pattern1_pattern1_i4_url ) | No | object | No | In #/definitions/InputURI | The URL(s) / URI(s) where this input is available | | - [secondary-urls](#params_pattern1_pattern1_i4_secondary-urls ) | No | object | No | Same as [url](#params_pattern1_pattern1_i4_url ) | Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept) | | - [preferred-name](#params_pattern1_pattern1_i4_preferred-name ) | No | boolean or string | No | - | Preferred base name / relative path for this input, instead of the derived one from the URL | | - [relative-dir](#params_pattern1_pattern1_i4_relative-dir ) | No | boolean or string | No | - | Put contents fetched for this input in this relative directory. This option does not affect preferred-name | | - [security-context](#params_pattern1_pattern1_i4_security-context ) | No | string | No | - | Use an explicitly named security context | | - [disclosable](#params_pattern1_pattern1_i4_disclosable ) | No | boolean | No | - | Whether this input contents can be included in RO-Crates or exported | | - [cacheable](#params_pattern1_pattern1_i4_cacheable ) | No | boolean | No | - | Whether a copy of this input contents can be kept locally outside the working directory | | - [clonable](#params_pattern1_pattern1_i4_clonable ) | No | boolean | No | - | Whether a copy of this input contents can be kept locally inside the working directory | | - [globExplode](#params_pattern1_pattern1_i4_globExplode ) | No | string | No | - | When this is set, and the class is directory, it helps filtering in what it should be included | | - [autoFill](#params_pattern1_pattern1_i4_autoFill ) | No | boolean | No | - | When this key is true, the directory or file is considered an output one | | - [autoPrefix](#params_pattern1_pattern1_i4_autoPrefix ) | No | boolean | No | - | When autoFill is true and this parameter is false, this directory is mapped to the parent output one for this execution. When both autoFill and this parameter are true, an output file or directory name is assigned, based on its complete param name | | All of(Requirement) | | ----------------------------------------------- | | [item 0](#params_pattern1_pattern1_i4_allOf_i0) | | [item 1](#params_pattern1_pattern1_i4_allOf_i1) | | [item 2](#params_pattern1_pattern1_i4_allOf_i2) | | [item 3](#params_pattern1_pattern1_i4_allOf_i3) | | [item 4](#params_pattern1_pattern1_i4_allOf_i4) | | [item 5](#params_pattern1_pattern1_i4_allOf_i5) | | [item 6](#params_pattern1_pattern1_i4_allOf_i6) | | [item 7](#params_pattern1_pattern1_i4_allOf_i7) | ##### 9.1.5.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 0` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.1.1. If (c-l-a-s-s = Must be one of: * "Directory" * "File" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.1.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.1.1.1.1. The following properties are required * value * tabular * autoFill * autoPrefix ##### 9.1.5.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 1` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.2.1. If (c-l-a-s-s = "ContentWithURIs" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.2.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.2.1.1.1. The following properties are required * value * autoFill * autoPrefix ##### 9.1.5.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 2` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.3.1. If (c-l-a-s-s = Must be one of: * "Directory" * "File" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.3.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.3.1.1.1. The following properties are required * value * tabular * url * secondary-urls * security-context * globExplode ##### 9.1.5.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 3` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.4.1. If (c-l-a-s-s = "Directory" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.4.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.4.1.1.1. The following properties are required * value ##### 9.1.5.5. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 4` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.5.1. If (c-l-a-s-s = "File" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.5.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.5.1.1.1. The following properties are required * url * tabular * secondary-urls * security-context * globExplode * autoFill * autoPrefix ##### 9.1.5.6. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 5` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.6.1. If (c-l-a-s-s = "ContentWithURIs" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.6.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.6.1.1.1. The following properties are required * url * secondary-urls * security-context * globExplode * autoFill * autoPrefix ##### 9.1.5.7. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 6` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.7.1. If (c-l-a-s-s = "Value" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.7.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.7.1.1.1. The following properties are required * tabular * url * secondary-urls * preferred-name * relative-dir * security-context * globExplode * autoFill * autoPrefix * cacheable * clonable ###### 9.1.5.7.1.2. The following properties are required * value ##### 9.1.5.8. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 7` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1. If (c-l-a-s-s = "ContentWithURIs" ) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1.1. The following properties are required * globExplode * autoFill * autoPrefix If(_complex condition_) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1.2. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1.2.1. The following properties are required * value IfNot(_complex condition_) | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1.3. Must **not** be | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | ###### 9.1.5.8.1.1.3.1. The following properties are required * url * secondary-urls * security-context ###### 9.1.5.8.1.1.4. The following properties are required * value ###### 9.1.5.8.1.2. The following properties are required * tabular ##### 9.1.5.9. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > c-l-a-s-s` | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | Yes | Must be one of: * "File" * "Directory" * "Value" * "ContentWithURIs" ##### 9.1.5.10. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** When 'c-l-a-s-s' is a single file or a value, the assigned value | One of(Option) | | ----------------------------------------------------- | | [item 0](#params_pattern1_pattern1_i4_value_oneOf_i0) | | [item 1](#params_pattern1_pattern1_i4_value_oneOf_i1) | ###### 9.1.5.10.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 0` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | -------------- | - | | **Min length** | 1 | ###### 9.1.5.10.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1` | | | | ------------ | ----------------- | | **Type** | `array of string` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | ----------------------------------------------------------------- | ----------- | | [item 1 items](#params_pattern1_pattern1_i4_value_oneOf_i1_items) | - | ###### 9.1.5.10.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1 > item 1 items | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | -------------- | - | | **Min length** | 1 | ##### 9.1.5.11. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** When it is content with URIs, we are telling it is a tabular one with this key. URIs are fetched, and the absolute paths replace them in the generated content tab | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ------------------------------------------------------------------ | ------- | ---------------- | ---------- | ---------- | --------------------------------------------------------------------- | | + [uri-columns](#params_pattern1_pattern1_i4_tabular_uri-columns ) | No | array of integer | No | - | The columns where URIs to be fetched are found | | - [row-sep](#params_pattern1_pattern1_i4_tabular_row-sep ) | No | enum (of string) | No | - | The string used to split the tabulated content by rows | | + [column-sep](#params_pattern1_pattern1_i4_tabular_column-sep ) | No | string | No | - | The regular expression used to split the tabulated content by columns | | - [header-rows](#params_pattern1_pattern1_i4_tabular_header-rows ) | No | integer | No | - | How many header rows should be skipped? | ###### 9.1.5.11.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns` | | | | ------------ | ------------------ | | **Type** | `array of integer` | | **Required** | Yes | **Description:** The columns where URIs to be fetched are found | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | True | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | --------------------------------------------------------------------------- | ----------- | | [uri-columns items](#params_pattern1_pattern1_i4_tabular_uri-columns_items) | - | ###### 9.1.5.11.1.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns > uri-columns items | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | ###### 9.1.5.11.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > row-sep` | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | No | | **Default** | `"\n"` | **Description:** The string used to split the tabulated content by rows Must be one of: * "\n" * "\r" * "\t\n" | Restrictions | | | -------------- | - | | **Min length** | 1 | ###### 9.1.5.11.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > column-sep` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | Yes | **Description:** The regular expression used to split the tabulated content by columns | Restrictions | | | -------------- | - | | **Min length** | 1 | ###### 9.1.5.11.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > header-rows` | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | **Default** | `0` | **Description:** How many header rows should be skipped? ##### 9.1.5.12. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | **Defined in** | #/definitions/InputURI | **Description:** The URL(s) / URI(s) where this input is available | One of(Option) | | ----------------------------------------------------------- | | [PlainURI](#params_pattern1_pattern1_i4_url_oneOf_i0) | | [PlaceholderURI](#params_pattern1_pattern1_i4_url_oneOf_i1) | | [LicensedURI](#params_pattern1_pattern1_i4_url_oneOf_i2) | | [item 3](#params_pattern1_pattern1_i4_url_oneOf_i3) | ###### 9.1.5.12.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlainURI` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [trs_endpoint](#trs_endpoint) | ###### 9.1.5.12.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlaceholderURI` | | | | -------------- | ---------------------------- | | **Type** | `string` | | **Required** | No | | **Defined in** | #/definitions/PlaceholderURI | | Restrictions | | | --------------------------------- | ----------------------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```$\{[^}]+\}``` [Test](https://regex101.com/?regex=%24%5C%7B%5B%5E%7D%5D%2B%5C%7D) | ###### 9.1.5.12.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > LicensedURI` | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Defined in** | #/definitions/LicensedURI | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | --------------------------------------------------------------------------------- | ------- | --------------- | ---------- | ---------- | ----------------------- | | + [uri](#params_pattern1_pattern1_i4_url_oneOf_i2_uri ) | No | Combination | No | - | The URI of the resource | | - [licences](#params_pattern1_pattern1_i4_url_oneOf_i2_licences ) | No | array | No | - | - | | - [attributions](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions ) | No | array of object | No | - | - | | - [security-context](#params_pattern1_pattern1_i4_url_oneOf_i2_security-context ) | No | string | No | - | - | ###### 9.1.5.12.3.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | Yes | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** The URI of the resource | Any of(Option) | | ------------------------------------------------------------------------ | | [PlainURI](#params_pattern1_pattern1_i4_url_oneOf_i2_uri_anyOf_i0) | | [PlaceholderURI](#params_pattern1_pattern1_i4_url_oneOf_i2_uri_anyOf_i1) | ###### 9.1.5.12.3.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlainURI` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [trs_endpoint](#trs_endpoint) | ###### 9.1.5.12.3.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlaceholderURI` | | | | ---------------------- | ------------------------------------------------------------------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [params_pattern1_pattern1_i4_url_oneOf_i1](#params_pattern1_pattern1_i4_url_oneOf_i1) | ###### 9.1.5.12.3.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences` | | | | ------------ | ------- | | **Type** | `array` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | -------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------- | | [PlainURI](#params_pattern1_pattern1_i4_url_oneOf_i2_licences_items) | URL to the description of the licence of the data. And by default, no permission to use or distribute it | ###### 9.1.5.12.3.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences > PlainURI | | | | -------------- | --------------------------------------------- | | **Type** | `string` | | **Required** | No | | **Default** | `"https://choosealicense.com/no-permission/"` | | **Defined in** | #/definitions/PlainURI | **Description:** URL to the description of the licence of the data. And by default, no permission to use or distribute it | Restrictions | | | -------------- | - | | **Min length** | 1 | ###### 9.1.5.12.3.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions` | | | | ------------ | ----------------- | | **Type** | `array of object` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | True | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | ---------------------------------------------------------------------------------- | ----------- | | [attributions items](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items) | - | ###### 9.1.5.12.3.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ------------------------------------------------------------------------------ | ------- | ------------------------- | ---------- | -------------------------------------- | ------------------------------------------------------------------------------------------------------------- | | + [name](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_name ) | No | string | No | - | Name of the author | | + [pid](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_pid ) | No | string | No | Same as [trs_endpoint](#trs_endpoint ) | A unique way to represent this author, either through her/his ORCID or another permanent, representative link | | + [roles](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_roles ) | No | array of enum (of string) | No | - | - | ###### 9.1.5.12.3.3.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > name` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | Yes | **Description:** Name of the author | Restrictions | | | -------------- | - | | **Min length** | 1 | ###### 9.1.5.12.3.3.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > pid` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | Yes | | **Same definition as** | [trs_endpoint](#trs_endpoint) | **Description:** A unique way to represent this author, either through her/his ORCID or another permanent, representative link ###### 9.1.5.12.3.3.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles` | | | | ------------ | --------------------------- | | **Type** | `array of enum (of string)` | | **Required** | Yes | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | True | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | --------------------------------------------------------------------------------------- | ----------- | | [roles items](#params_pattern1_pattern1_i4_url_oneOf_i2_attributions_items_roles_items) | - | ###### 9.1.5.12.3.3.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles > roles items | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | No | Must be one of: * "conceptualization" * "data-curation" * "formal-analysis" * "funding-acquisition" * "investigation" * "methodology" * "project-administration" * "resources" * "software" * "supervision" * "validation" * "visualization" * "writing-original-draft" * "writing-review-editing" ###### 9.1.5.12.3.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > security-context` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | --------------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```^[^:;]+$``` [Test](https://regex101.com/?regex=%5E%5B%5E%3A%3B%5D%2B%24) | ###### 9.1.5.12.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3` | | | | ------------ | ------- | | **Type** | `array` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | --------------------------------------------------------------- | ----------- | | [item 3 items](#params_pattern1_pattern1_i4_url_oneOf_i3_items) | - | ###### 9.1.5.12.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | One of(Option) | | -------------------------------------------------------------------------- | | [LicensedURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i0) | | [PlainURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i1) | | [PlaceholderURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i2) | | [item 3](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3) | ###### 9.1.5.12.4.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > LicensedURI` | | | | ------------------------- | ------------------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Same definition as** | [params_pattern1_pattern1_i4_url_oneOf_i2](#params_pattern1_pattern1_i4_url_oneOf_i2) | ###### 9.1.5.12.4.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlainURI` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [trs_endpoint](#trs_endpoint) | ###### 9.1.5.12.4.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI` | | | | ---------------------- | ------------------------------------------------------------------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [params_pattern1_pattern1_i4_url_oneOf_i1](#params_pattern1_pattern1_i4_url_oneOf_i1) | ###### 9.1.5.12.4.1.4. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3` | | | | ------------ | ------- | | **Type** | `array` | | **Required** | No | **Description:** This element is an array of alternate URLs, so any of them provide the very same resources | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 2 | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | ------------------------------------------------------------------------------ | ----------- | | [item 3 items](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items) | - | ###### 9.1.5.12.4.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | One of(Option) | | ----------------------------------------------------------------------------------------- | | [LicensedURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i0) | | [PlainURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i1) | | [PlaceholderURI](#params_pattern1_pattern1_i4_url_oneOf_i3_items_oneOf_i3_items_oneOf_i2) | ###### 9.1.5.12.4.1.4.1.1. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > LicensedURI` | | | | ------------------------- | ------------------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Same definition as** | [params_pattern1_pattern1_i4_url_oneOf_i2](#params_pattern1_pattern1_i4_url_oneOf_i2) | ###### 9.1.5.12.4.1.4.1.2. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlainURI` | | | | ---------------------- | ----------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [trs_endpoint](#trs_endpoint) | ###### 9.1.5.12.4.1.4.1.3. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI` | | | | ---------------------- | ------------------------------------------------------------------------------------- | | **Type** | `string` | | **Required** | No | | **Same definition as** | [params_pattern1_pattern1_i4_url_oneOf_i1](#params_pattern1_pattern1_i4_url_oneOf_i1) | ##### 9.1.5.13. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > secondary-urls` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | **Same definition as** | [url](#params_pattern1_pattern1_i4_url) | **Description:** Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept) ##### 9.1.5.14. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > preferred-name` | | | | ------------ | ------------------- | | **Type** | `boolean or string` | | **Required** | No | | **Default** | `false` | **Description:** Preferred base name / relative path for this input, instead of the derived one from the URL | Restrictions | | | -------------- | - | | **Min length** | 1 | ##### 9.1.5.15. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > relative-dir` | | | | ------------ | ------------------- | | **Type** | `boolean or string` | | **Required** | No | | **Default** | `false` | **Description:** Put contents fetched for this input in this relative directory. This option does not affect preferred-name | Restrictions | | | -------------- | - | | **Min length** | 1 | ##### 9.1.5.16. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > security-context` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** Use an explicitly named security context | Restrictions | | | -------------- | - | | **Min length** | 1 | ##### 9.1.5.17. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > disclosable` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `true` | **Description:** Whether this input contents can be included in RO-Crates or exported ##### 9.1.5.18. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > cacheable` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `true` | **Description:** Whether a copy of this input contents can be kept locally outside the working directory ##### 9.1.5.19. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > clonable` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `true` | **Description:** Whether a copy of this input contents can be kept locally inside the working directory ##### 9.1.5.20. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > globExplode` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** When this is set, and the class is directory, it helps filtering in what it should be included ##### 9.1.5.21. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoFill` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `false` | **Description:** When this key is true, the directory or file is considered an output one ##### 9.1.5.22. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoPrefix` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | | **Default** | `false` | **Description:** When autoFill is true and this parameter is false, this directory is mapped to the parent output one for this execution. When both autoFill and this parameter are true, an output file or directory name is assigned, based on its complete param name #### 9.1.6. Property `WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > Params` | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Same definition as** | [params](#params) | ## 10. Property `WfExS-backend stage definition > profile` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | **Description:** For engines which support profiles, like Nextflow or snakemake, if defined, the profile/s to enable | One of(Option) | | --------------------------- | | [item 0](#profile_oneOf_i0) | | [item 1](#profile_oneOf_i1) | ### 10.1. Property `WfExS-backend stage definition > profile > oneOf > item 0` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$``` [Test](https://regex101.com/?regex=%5E%5B%5E%2C+%09%5D%2B%5B+%09%5D%2A%28%2C%5B+%09%5D%2A%5B%5E%2C+%09%5D%2B%5B+%09%5D%2A%29%2A%24) | ### 10.2. Property `WfExS-backend stage definition > profile > oneOf > item 1` | | | | ------------ | ----------------- | | **Type** | `array of string` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 1 | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | --------------------------------------- | ----------- | | [item 1 items](#profile_oneOf_i1_items) | - | #### 10.2.1. WfExS-backend stage definition > profile > oneOf > item 1 > item 1 items | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | | Restrictions | | | --------------------------------- | ----------------------------------------------------------------------- | | **Min length** | 1 | | **Must match regular expression** | ```^[^,]+$``` [Test](https://regex101.com/?regex=%5E%5B%5E%2C%5D%2B%24) | ## 11. Property `WfExS-backend stage definition > environment` | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ------------------------------------- | ------- | ------ | ---------- | ----------------------- | ---------------------------------------------------------------------------------------------------- | | - [^[^=\0]+$](#environment_pattern1 ) | Yes | object | No | In #/definitions/EnvVar | The name of an environment variable. These names cannot contain either the equal or the character \0 | ### 11.1. Pattern Property `WfExS-backend stage definition > environment > EnvVar` > All properties whose name matches the regular expression ```^[^=\0]+$``` ([Test](https://regex101.com/?regex=%5E%5B%5E%3D%5C0%5D%2B%24)) must respect the following conditions | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | **Defined in** | #/definitions/EnvVar | **Description:** The name of an environment variable. These names cannot contain either the equal or the character \0 | One of(Option) | | -------------------------------------------- | | [item 0](#environment_pattern1_pattern1_i0) | | [DirFile](#environment_pattern1_pattern1_i1) | #### 11.1.1. Property `WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > item 0` | | | | ------------ | ------------------ | | **Type** | `string or number` | | **Required** | No | #### 11.1.2. Property `WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > DirFile` | | | | ------------------------- | ----------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | **Same definition as** | [params_pattern1_pattern1_i4](#params_pattern1_pattern1_i4) | ## 12. Property `WfExS-backend stage definition > outputs` | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | -------------------------------- | ------- | ------ | ---------- | ---------- | ----------------- | | - [^[^:;]+$](#outputs_pattern1 ) | Yes | object | No | - | - | ### 12.1. Pattern Property `WfExS-backend stage definition > outputs > ^[^:;]+$` > All properties whose name matches the regular expression ```^[^:;]+$``` ([Test](https://regex101.com/?regex=%5E%5B%5E%3A%3B%5D%2B%24)) must respect the following conditions | | | | ------------------------- | ------------------------------------------------------- | | **Type** | `object` | | **Required** | No | | **Additional properties** | [[Not allowed]](# "Additional Properties not allowed.") | | Property | Pattern | Type | Deprecated | Definition | Title/Description | | ------------------------------------------------------- | ------- | ---------------- | ---------- | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | + [c-l-a-s-s](#outputs_pattern1_c-l-a-s-s ) | No | enum (of string) | No | - | - | | - [cardinality](#outputs_pattern1_cardinality ) | No | Combination | No | - | Output cardinality | | - [preferredName](#outputs_pattern1_preferredName ) | No | string | No | - | Preferred name for this output, honored when either filledFrom or glob are used | | - [fillFrom](#outputs_pattern1_fillFrom ) | No | string | No | - | Autofilled input from where to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake) | | - [syntheticOutput](#outputs_pattern1_syntheticOutput ) | No | boolean | No | - | Is this output a synthetic one? The default value when it is not defined depends on the type of workflow. | | - [glob](#outputs_pattern1_glob ) | No | string | No | - | Glob pattern to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake) | #### 12.1.1. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > c-l-a-s-s` | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | Yes | Must be one of: * "File" * "Directory" #### 12.1.2. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality` **Title:** Output cardinality | | | | ------------------------- | ------------------------------------------------------------------------- | | **Type** | `combining` | | **Required** | No | | **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | | **Default** | `1` | **Description:** Expected cardinality of this output | One of(Option) | | ------------------------------------------------ | | [item 0](#outputs_pattern1_cardinality_oneOf_i0) | | [item 1](#outputs_pattern1_cardinality_oneOf_i1) | | [item 2](#outputs_pattern1_cardinality_oneOf_i2) | ##### 12.1.2.1. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 0` | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | No | Must be one of: * "1" * "?" * "*" * "+" ##### 12.1.2.2. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 1` | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 0 | ##### 12.1.2.3. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2` | | | | ------------ | ------- | | **Type** | `array` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | 2 | | **Max items** | 2 | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | See below | | Each item of this array must be | Description | | ---------------------------------------------------------------- | ----------- | | [item 2 item 0](#outputs_pattern1_cardinality_oneOf_i2_items_i0) | - | | [item 2 item 1](#outputs_pattern1_cardinality_oneOf_i2_items_i1) | - | ###### 12.1.2.3.1. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 0 | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 0 | ###### 12.1.2.3.2. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 1 | | | | ------------ | --------- | | **Type** | `integer` | | **Required** | No | | Restrictions | | | ------------ | ------ | | **Minimum** | ≥ 1 | #### 12.1.3. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > preferredName` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** Preferred name for this output, honored when either filledFrom or glob are used | Restrictions | | | -------------- | - | | **Min length** | 1 | #### 12.1.4. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > fillFrom` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** Autofilled input from where to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake) | Restrictions | | | -------------- | - | | **Min length** | 1 | #### 12.1.5. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > syntheticOutput` | | | | ------------ | --------- | | **Type** | `boolean` | | **Required** | No | **Description:** Is this output a synthetic one? The default value when it is not defined depends on the type of workflow. #### 12.1.6. Property `WfExS-backend stage definition > outputs > ^[^:;]+$ > glob` | | | | ------------ | -------- | | **Type** | `string` | | **Required** | No | **Description:** Glob pattern to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake) | Restrictions | | | -------------- | - | | **Min length** | 1 | ## 13. Property `WfExS-backend stage definition > default_actions` | | | | ------------ | ------- | | **Type** | `array` | | **Required** | No | | | Array restrictions | | -------------------- | ------------------ | | **Min items** | N/A | | **Max items** | N/A | | **Items unicity** | False | | **Additional items** | False | | **Tuple validation** | N/A | ---------------------------------------------------------------------------------------------------------------------------- Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-09-19 at 23:38:46 +0000