Workflows and Analyses

A workflow is a container that organizes multiple executable components (apps or applets) along with their configuration settings. Think of a workflow as a pipeline that connects multiple tools together. For example, a DNA sequencing workflow might include three apps in sequence: mapping, variant calling, and variant annotation. You can configure outputs from one component to feed directly into the next. Each component in a workflow, along with its settings and input/output parameters, is called a stage. You cannot use workflows as stages within other workflows.

An analysis is what happens when you run a workflow—similar to how a job runs when you execute an app. Both jobs and analyses can be referred to as runs of their respective executables.

To create a new workflow, use the /workflow/new API method. You can modify the workflow with specific API methods that support different types of edits. When ready, run the workflow with the /workflow-xxxx/run API method. This creates an analysis object that tracks all the jobs (and potentially other analyses) created during execution.

After creating an analysis, you can recreate the original workflow by calling /workflow/new with the initializeFrom parameter set to the analysis ID.

For information on building or managing Nextflow workflows, see Running Nextflow Pipelines.

Editing a Workflow

A workflow object has an edit version number which can be retrieved using the API call /workflow-xxxx/describe. It must be provided every time an API call is made to edit a workflow and must match the current value to succeed. The new edit version number is returned on a successful edit.

Managing Stages

You can specify what stages should be run when creating the workflow using /workflow/new. You can also add additional stages after creating the workflow with /workflow-xxxx/addStage. When adding a stage, you must specify the executable to run. You must also specify a unique stage ID. However, when adding stages to an already existing workflow with /workflow-xxxx/addStage, the ID is optional, and if you do not supply it, a unique ID is generated on your behalf (see the section Stage ID and Name for more information).

This ID is unique for the stage in the workflow. You need to provide it when making further changes to the stage or cross-linking outputs and inputs of the stages.

Besides the executable that it runs, each stage can also have the following metadata:

Name
Output folder
Default input values
IO spec modifications that are exported for the workflow
Execution Policy
System Requirements

Most of the above options can also be set when the stage is created and can always be modified afterwards via the /workflow-xxxx/update method.

Stages can be reordered or removed using the /workflow-xxxx/moveStage and /workflow-xxxx/removeStage API methods. As mentioned previously, both the stage ID and the workflow's edit version need to be provided to modify them.

Replacing the executable of a stage in-place (keeping all other metadata associated with the stage such as its name, output folder, bound inputs, and configuration settings), can only be done using the /workflow-xxxx/updateStageExecutable API method. This method tests whether the replacement candidate has input and output specifications which are fully compatible with the previous executable if it is still accessible. If it is not fully compatible, it can still be updated by setting the force flag to true, in which case the workflow is also updated to remove any outdated links between stages and other such outdated metadata.

Stage ID and Name

A stage ID uniquely identifies the stage within a workflow and allows inputs and outputs of different stages to be linked to each other. When adding a stage (either in /workflow/new or /workflow-xxxx/addStage) you must supply a unique ID to identify each stage. As an exception, in /workflow-xxxx/addStage it is not mandatory to supply an ID. If you do not do so, an arbitrary unique ID is generated on your behalf.

Stage IDs must match the regular expression ^[a-zA-Z_][0-9a-zA-Z_-]{0,255}$ (only letters, numbers, underscores, and dashes, at least one char, does not start with a number or dash. Maximum length is 256 characters).

The stage name is a non-unique label used for display purposes. It allows you to provide a descriptive identifier for the stage that is shown in the UI in the workflow view. If not provided, the executable's name is displayed instead.

Customizing Output Folders

The workflow can have a default output folder which is set by its outputFolder field (either at workflow creation time or through the /workflow-xxxx/update method). This value can be overridden at runtime using the folder field. If no value for the output folder can be found in the API call nor in the workflow, then the system default of "/" is used.

Stage Output Folders

Each stage can also specify its default output folder. This can be defined relative to the workflow's output folder, or as an absolute path. This field can be set in the /workflow-xxxx/addStage method and further updated using the /workflow-xxxx/update method.

If the value set for the stage's folder field starts with the character "/", then this is interpreted as an absolute path that is used for the stage's outputs, regardless of what is provided as folder in the /workflow-xxxx/run method.

If, however, the value set for the field does not start with the character "/", then it is interpreted as a path relative to the field folder provided to /workflow-xxxx/run method.

The following table shows some examples for where a stage's output goes for different values of the stage's folder field, under the condition that the workflow's output folder is "/foo":

Stage's folder Value

Stage Output Folder

null (no value)

"/foo"

"bar/baz"

"/foo/bar/baz"

"/quux"

Workflow Input and Output (Locked Workflows)

Workflow Input

It is possible to define an explicit input to the workflow by specifying inputs for the /workflow/new method, for example:

{
  "inputs": [
    {
      "name": "reference_genome",
      "class": "file"
    }
  ]
}

One consequence of defining a workflow with an explicit input is that once the workflow is created, all the input values need to be provided by the user to workflow inputs and not to stages. By linking stage inputs with workflow inputs during workflow build time, all the values provided to a workflow-level input (here reference_genome) are passed during execution to the stage-level inputs that link to it.

Defining inputs for the workflow creates a special type of a workflow called locked workflow. Locked workflows are workflows in which certain input fields cannot be overridden when the workflow is initialized to run. This is achieved by the inputs property, which acts as an allowable list for those inputs which are "unlocked". If the workflow creator defines this property, the inputs listed in this array can be set by the user when they run the workflow (they are considered "unlocked"), and all other inputs are automatically "locked". When the inputs property is undefined or null the workflow is fully unlocked and acts like any other regular workflow where all the inputs can be provided or overridden by the user that runs the workflow. When the inputs property is set to an empty array, there are no unlocked fields so the workflow is fully locked.

Workflow Output

The outputs of the stages can be defined to be the output of the workflow. To do that, the field outputs needs to be passed to /workflow/new, which defines references to stages' outputs in outputSource. For example, if we'd like the output of the workflow to be the output of "outputFieldName" of the stage stage-xxxx, but the output of other stages are of no interest to us, we can define it in the following way:

{
  "outputs": [
    {
      "name": "pipeline_output",
      "class": "array:file",
      "outputSource": {
        "$dnanexus_link": {
          "stage": "stage-xxxx",
          "outputField": "output_field_of_stage_xxxx"
        }
      }
    }
  ]
}

Binding Input

When adding an executable as a stage or modifying it using the /workflow-xxxx/update API method, you can choose to specify values for the stage inputs. These bound inputs can be overridden when the workflow is actually run. The syntax for providing bound input is the same as when providing an input hash to run the executable directly. For example, you can set the input for a stage with the hash:

{ "input_field": "input_value" }

You can also use stage references as values to link an input to the input or output of another stage. These references are hashes with a single key $dnanexus_link whose value is a hash with exactly two keys/values:

stage string another stage's ID whose output is used

exactly one of the following key/values:

outputField string the output field name of the stage's executable to be used
inputField string the input field name of the stage's executable to be used

and, optionally:

index integer the index of the array that is the output or input of the linked stage. This is 0-indexed, so a value of 0 indicates the first element should be used.

If the workflow has defined inputs, you can use workflow input references to link stage inputs to the workflow level inputs. These references are hashes with a singe key $dnanexus_link whose value is a hash with exactly one key/value:

workflowInputField: string the input field name of the current workflow

Linking input to other stage output

Using the outputField option is useful for chaining the output of a stage to the input of another stage to make an analysis pipeline. For example, a first stage (stage-xxxx) could maps reads to a reference genome and then pass those mappings on to a second stage (stage-yyyy) that calls variants on those mappings. We can do this by setting the following input for the second stage:

{
  "mappings_input_field_of_stage_yyyy": {
    "$dnanexus_link": {
      "stage": "stage-xxxx",
      "outputField": "mappings_output_field_of_stage_xxxx"
    }
  }
}

When the workflow is run, the second stage receives the mappings input once the first stage has finished.

Linking input to other stage input

Linking input fields together can also be useful. For example, if there are two stages which require the same reference genome, we can link the input of one (stage-xxxx) to the other (stage-yyyy) by setting the input of the first as follows:

{
  "reference_genome_field_of_stage_xxxx": {
    "$dnanexus_link": {
      "stage": "stage-yyyy",
      "inputField": "reference_genome_field_of_stage_yyyy"
    }
  }
}

When running the workflow, the reference genome input only needs to be provided once to the input of stage-yyyy, and the other stage stage-xxxx inherits the same value.

Linking workflow input to stage input

It is possible to link stage input to the input of the current workflow. For example, if the stage-xxxx requires a reference genome, we can link the input of stage-xxxx to the input of the workflow as follows:

{
  "reference_genome_field_of_stage_xxxx": {
    "$dnanexus_link": {
      "workflowInputField": "reference_genome"
    }
  }
}

The workflow inputs field should then be defined for the workflow, for example:

{
  "inputs": [
    {
      "name": "reference_genome",
      "class": "file"
    }
  ]
}

During runtime, the stage inputs consume the input values provided on the workflow level. That is, the value passed to the field reference_genome is used by reference_genome_field_of_stage_xxxx.

See the section on Workflow input and output for more information.

Customizing IO Specifications

The /workflow-xxxx/update API method can also be used to modify how an input or output to a stage can be represented as an input or output of the workflow. For example, a particular input parameter can be hidden so that it does not appear in the inputSpec field when describing the workflow. Or, it can be given a name (unique in the workflow) so that its stage does not have to be specified when providing input to the workflow. Its label or help can also be changed to document how it may interact with other stages in the workflow.

Hiding an output for a stage means the output is treated as intermediate output and is deleted after the analysis has finished running.

Execution Policy

Each stage can have an executionPolicy field to request the value to be passed on when the stage is run (see the executionPolicy field in the run specification of apps and applets for the accepted options).

These stored execution policies can also change the failure propagation behavior. By default, if a stage fails, the entire analysis enters the partially_failed state, and other stages are allowed to finish successfully if they are not dependent on the failed stage. This behavior can be modified to propagate failure to all other stages by setting the onNonRestartableFailure flag in the executionPolicy field for an individual stage to have value "failAllStages". These stage-specific options can also be overridden at runtime by providing a single value to be used by all stages in the /workflow-xxxx/run call.

System Requirements

Each stage of the workflow can have a systemRequirements field to request certain instance types by default when the workflow is run. This field uses the same syntax as used in the run specification for applets and apps. This value can be set when the stage is added or modified afterwards with the /workflow-xxxx/update API method.

These stored defaults can be further overridden (in part or in full) at runtime by providing some combination of systemRequirementsByExecutable, systemRequirements and stageSystemRequirements fields in /workflow-xxxx/run. A stage's stored value for systemRequirements remains active for a specific entry point unless explicitly overridden with a new value for that entry point, or implicitly overridden via a value for the "*" entry point. Refer to the information in Requesting Instance Types for more details.

Reuse of Previous Results

A license is required to use the Smart Reuse feature. Contact DNAnexus Sales for more information.

When running a workflow, if the Smart Reuse feature has been enabled, the system attempts to reuse previously computed results by looking up analyses that have been created for the workflow. To find out which stages have cached results on hand without running the workflow, you can call the /workflow-xxxx/dryRun method or with /workflow-xxxx/describe method with getRerunInfo set to true. To turn off this automatic behavior, you can request that certain stages be forcibly rerun using rerunStages in the /workflow-xxxx/run method.

See this documentation for more on this feature.

Analysis Input

When specifying input for /workflow-xxxx/run, the input field names for an analysis are automatically generated to have the form "<stage ID>.<input field name>" if the input is provided to a stage directly, or "<input field name>" if it is the input defined for the workflow.

For example, if the first stage has ID "stage-xxxx" and would run an executable which takes in an input named "reads", then to provide the input for this parameter, you would use the key "stage-xxxx.reads" in the input hash. These names can be renamed via the API call /workflow-xxxx/update using the stages.stage-xxxx.inputSpecMods field.

Connecting the input to the input or output of another stage in the workflow is also possible. In such a situation, a workflow stage reference should be used. To reference the input of another stage, say of stage "stage-xxxx" with input "reference_genome", you would provide the value:

{ "$dnanexus_link": {
    "stage": "stage-xxxx",
    "inputField": "reference_genome"
  }
}

When the workflow is run, this is translated into whatever value is given as input for "reference_genome" for the stage "stage-xxxx" in the workflow.

If the key outputField is used in place of inputField, then the value represents the output of that stage instead. When the workflow is run and an analysis created, the workflow stage reference is translated into an analysis stage reference:

{ "$dnanexus_link": {
    "analysis": "analysis-xxxx",
    "stage": "stage-xxxx",
    "field": "reference_genome"
  }
}

which is resolved when the stage "stage-xxxx" finishes running in analysis "analysis-xxxx".

Workflow API Method Specifications

API method: `/workflow/new`

Specification

Creates a new workflow data object which can be used to execute a series of apps, applets, and/or workflows.

Inputs

project string ID of the project or container to which the workflow should belong, such as "project-xxxx".
name string (optional, default is the new ID) The name of the object
title string or null (optional, default null) Title of the workflow, for example, "Micro Map Pipeline". If null, then the name of the workflow is used as the title
summary string (optional, default "") A short description of the workflow
description string (optional, default "") A longer description about the workflow
outputFolder string (optional) The default output folder for the workflow. See the Customizing Output Folders section above for more details on how it interacts with stages' output folders
tags array of strings (optional) Tags to associate with the object
types array of strings (optional) Types to associate with the object
hidden boolean (optional, default false) Whether the object should be hidden
properties mapping (optional) Properties to associate with the object
- key Property name
- value string Property value
details mapping or array (optional, default { }) JSON object or array that is to be associated with the object. See the Object Details section for details on valid input
folder string (optional, default "/") Full path of the folder that is to contain the new object
parents boolean (optional, default false) Whether all folders in the path provided in folder should be created if they do not exist
inputs array of mappings (optional) An input specification of the workflow as described in the Input Specification section
outputs array of mappings (optional) An output specification of the workflow as described in the Output Specification section with an additional field specifying outputSource. See the Workflow output section for details
initializeFrom mapping (optional) Indicate an existing workflow or analysis from which to use the metadata as default values for all fields that are not given:
- id string ID of the workflow or analysis from which to retrieve workflow metadata
- project string (required for workflow IDs and ignored otherwise) ID of the project in which the workflow specified in id should be found
stages array of mappings (optional) Stages to add to the workflow. If not supplied, the workflow that is created is empty. Each value is a mapping with the key/values:
- id string ID that uniquely identifies the stage. See the section on Stage ID and Name for more information
- executable string ID of app or applet to be run in this stage
- name string (optional) Name (display label) for the stage
- folder string (optional, default is null) The output folder into which outputs should be cloned for the stage. See the Customizing Output Folders section above for more details
- input mapping (optional) The inputs to this stage to be bound. See the section on Binding Input for more information.
  - key Input field name
  - value Input field value
- executionPolicy mapping (optional) A collection of options that govern automatic job restart on certain types of failures. This can only be set at the user-level API call (jobs cannot override this for their subjobs). Contents of this field override any of the corresponding keys in the executionPolicy mapping found in the executable's run specification (if present). Includes the following optional key/values:
  - restartOn mapping (optional) Indicate a job restart policy
    key A restartable failure reason (ExecutionError, UnresponsiveWorker, JMInternalError, AppInternalError, JobTimeoutExceeded, or SpotInstanceInterruption) or * to indicate all restartable failure reasons that are otherwise not present as keys
    value int Maximum number of restarts for the failure reason
  - maxRestarts int (optional, default 9) Non-negative integer less than 10, indicating the maximum number of times that the job is restarted
  - onNonRestartableFailure string (optional, default failStage) Either the value failStage or failAllStages. Indicates whether the failure of this stage (when run as part of an analysis) should force all other non-terminal stages in the analysis to fail as also if a non-restartable failure occurs, even if those stages do not have any dependencies on this stage. (Stages that have dependencies on this stage still fail irrespective of this setting.)
- systemRequirements mapping (optional) Request specific resources for the stage's executable. See the Requesting Instance Types section for more details
ignoreReuse array of strings (optional) Specifies ids of workflow stages (or "*" for all stages) that ignore job reuse. If a specified stage points to a nested sub-workflow, reuse is ignored recursively by the whole nested sub-workflow. Overrides ignoreReuse setting in stage executables.
nonce string (optional) Unique identifier for this request. Ensures that even if multiple requests fail and are retried, only a single workflow is created. For more information, see Nonces.
treeTurnaroundTimeThreshold integer (optional, default: The treeTurnaroundTimeThreshold field of the initializeFrom workflow if the billTo of the project has jobNotifications enabled and initializeFrom is not N/A, otherwise N/A, with N/A meaning not available.) The turnaround time threshold (in seconds) for trees (specifically, root executions) that run this executable. See Job Notifications for more information about turnaround time and managing job notifications.

A license is required to use the jobNotifications feature. Contact DNAnexus Sales to enable jobNotifications.

Outputs

id string ID of the created workflow object, such as "workflow-xxxx".
editVersion int The initial edit version number of the workflow object

Errors

InvalidInput
- A reserved linking string ($dnanexus_link) appears as a key in a hash in "details" but is not the only key in the hash
- A reserved linking string ($dnanexus_link) appears as the only key in a hash in details but has value other than a string
- The id given under initializeFrom is not a valid workflow or analysis ID
- "project" is missing if id given under initializeFrom is a workflow ID
- For each property key-value pair, the size, encoded in UTF-8, of the property key may not exceed 100 bytes and the property value may not exceed 700 bytes
- A nonce was reused in a request but other inputs had changed signifying a new and different request
- A nonce may not exceed 128 bytes
InvalidType
- The project is not a valid project ID
PermissionDenied
- CONTRIBUTE access required, VIEW access required for the project specified under initializeFrom if a workflow or analysis was specified.
ResourceNotFound
- The specified project is not found
- The path in folder does not exist while parents is false, or a specified project, workflow, or analysis ID specified in initializeFrom is not found, or a stage in ignoreReuse is not found)

API method: `/workflow-xxxx/overwrite`

Specification

Overwrites the workflow with the workflow-specific metadata from another workflow or an analysis other than the editVersion. The workflow's name, tags, properties, types, visibility, and details are left unchanged.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
from mapping Indicate the existing workflow or analysis from which to use the metadata
- id string ID of the workflow or analysis from which to retrieve workflow metadata
- project string (required for workflow IDs and ignored otherwise) ID of the project ID in which the workflow specified in id should be found

Outputs

id string ID of the manipulated workflow
editVersion int The new edit version number

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- from is not a hash
- from.id is not a string
- from.project is not a string if from.id is a workflow ID
ResourceNotFound
- The specified workflow does not exist
- The workflow or analysis specified in from cannot be found
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project
- User does not have VIEW access to the project containing the workflow or analysis represented in from

API method: `/workflow-xxxx/addStage`

Specification

Adds a stage to the workflow.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
id string (optional) ID that uniquely identifies the stage. If not provided, a system-generated stage ID is set. See the section on Stage ID and Name for more information
executable string App or applet ID
name string or null (optional, default null) Name (display label) for the stage, or null to indicate no name
folder string (optional, default is null) The output folder into which outputs should be cloned for the stage. See the Customizing Output Folders section above for more details
input mapping (optional) A subset of the inputs to this stage to be bound. See the section on Binding Input for more information. key Input field name value Input field value
executionPolicy mapping (optional) A collection of options that govern automatic job restart on certain types of failures. This can only be set at the user-level API call (jobs cannot override this for their subjobs). Contents of this field override any of the corresponding keys in the executionPolicy mapping found in the executable's run specification (if present). Includes the following optional key/values:
- restartOn mapping (optional) Indicate a job restart policy
  - key A restartable failure reason (ExecutionError, UnresponsiveWorker, JMInternalError, AppInternalError, JobTimeoutExceeded, or SpotInstanceInterruption) or * to indicate all restartable failure reasons that are otherwise not present as keys
  - value int Maximum number of restarts for the failure reason
- maxRestarts int (optional, default 9) Non-negative integer less than 10, indicating the maximum number of times that the job is restarted
- onNonRestartableFailure string (optional, default failStage) Either the value failStage or failAllStages. Indicates whether the failure of this stage (when run as part of an analysis) should force all other non-terminal stages in the analysis to fail as also if a non-restartable failure occurs, even if those stages do not have any dependencies on this stage. (Stages that have dependencies on this stage still fail irrespective of this setting.)
systemRequirements mapping (optional) Request specific resources for the stage's executable. See the Requesting Instance Types section for more details

Outputs

id string ID of the manipulated workflow
editVersion int The new edit version number
stage string ID of the new stage

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- executable is not a string
- name if provided is not a string
- folder if provided is not a valid folder path
- input if provided is not a hash or is not valid input for the specified executable
- executionPolicy if provided is not a hash
- executionPolicy.restartOn if provided is not a hash, contains a failure reason key that cannot be restarted, or contains a value which is not an integer between 0 and 9
- executionPolicy.onNonRestartableFailure is not one of the allowed values
ResourceNotFound
- The specified workflow does not exist
- The specified executable does not exist
- A provided input value in input could not be found
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project
- An accessible copy of the executable could not be found

API method: `/workflow-xxxx/removeStage`

Specification

Removes a stage from the workflow.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
stage string ID of the stage to remove

Outputs

id string ID of the manipulated workflow
editVersion int The new edit version number

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- stage is not a string
ResourceNotFound
- The specified workflow does not exist
- The specified stage does not exist in the workflow
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project

API method: `/workflow-xxxx/moveStage`

Specification

Reorders the stages by moving a specified stage to a new index or position in the workflow. This does not affect how the stages are run but is merely for personal preference and organization.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
stage string ID of the stage to move
newIndex int The index or key that the stage has after the move. All other stages are moved to accommodate this change. Must be in [0, n), where n is the total number of stages

Outputs

id string ID of the manipulated workflow
editVersion int The new edit version number

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- stage is not a string
- newIndex is not in the range [0, n) where is the number of stages in the workflow
ResourceNotFound
- The specified workflow does not exist
- The specified stage does not exist in the workflow)
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project

API method: `/workflow-xxxx/update`

Specification

Update the workflow with any fields that are provided.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
title string or null (optional) The workflow's title, for example, "Micro Map Pipeline". If null, the name of the workflow is used as the title
summary string (optional) A short description of the workflow
description string (optional) A longer description about the workflow
outputFolder string or null (optional) The default output folder for the workflow, or null to unset. See the Customizing Output Folders section above for more details on how it interacts with stages' output folders
inputs array of mappings or null (optional) An input specification of the workflow as described in the Input Specification section
outputs array of mappings or null (optional) An output specification of the workflow as described in the Output Specification section with an additional field specifying outputSource. See the Workflow output section for details
stages mapping (optional) Updates for one or more of the workflow's stages
- key ID of the stage to update
- value mapping Updates to make to the stage
  - name string or null (optional) New name for the stage. Use null to unset the name
  - folder string or null (optional) The output folder into which outputs should be cloned for the stage. See the Customizing Output Folders section above for more details. Use null to unset the folder
  - input mapping (optional) A subset of the inputs to this stage to be bound or unbound (using null to unset a previously-bound input). See the section on Binding Input for more information. key Input field name from this stage's executable value Input field value, or null to unset
  - executionPolicy mapping (optional) Set the default execution policy for this stage. Use the empty mapping { } to unset
  - stageRequirements mapping (optional) Request specific resources for the stage's executable. See the Requesting Instance Types section for more details. Use the empty mapping { } to unset
  - inputSpecMods mapping (optional) Updates to how the stage input specification is exported for the workflow. Any subset can be provided
    key Input field name from this stage's executable
    value mapping Updates for the specified stage input field name
    name string or null (optional) The canonical name by which a stage's input can be addressed when running the workflow is of the form "<stage ID>.<original field name>". By providing a different string here, you override the name as shown in the inputSpec of the workflow, and it can be used when giving input to run the workflow. The canonical name value can still be used to refer to this input, but both names cannot be used simultaneously. If null is provided, then any previously-set name is dropped. Only the canonical name can be used.
    label string or null (optional) A replacement label for the input parameter. If null is provided, then any previously-set label is dropped. The original executable's label is used.
    help string or null (optional) A replacement help string for the input parameter. If null is provided, then any previously-set help string is dropped and the original executable's help string is used.
    group string or null (optional) A replacement group for the input parameter. The default group for a stage's input is the stage's ID (if it had no group in the executable), or the string "<stage ID>:<group name>" (if it was part of a group in the executable). By providing a different string here, you override the group in which the input parameter appears in the inputSpec of the workflow. If the null value is provided, then any previously-set group value is dropped. The canonical group name is used. If the empty string is provided, the parameter is not in any group.
    hidden boolean (optional) Whether to hide the input parameter from the inputSpec of the workflow. The input can still be provided and overridden by its name "<stage ID>.<original field name>".
  - outputSpecMods mapping (optional) Updates to how the stage output specification is exported for the workflow. Any subset can be provided. This field follows the same syntax as for inputSpecMods defined above and behaves roughly the same but modifies outputSpec instead. The exception in behavior occurs for the hidden field. If an output has hidden set to true, its data object value (if applicable) is not cloned into the parent container when the stage or analysis is done. This may be a useful feature if a stage in your analysis produces many intermediate outputs that are not relevant to the analysis or are not ultimately useful once the analysis has finished.

Outputs

id string ID of the manipulated workflow
editVersion int The new edit version number

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- title if provided is not a string nor null
- summary if provided is not a string
- description if provided is not a string
- stages if provided is not a hash
- A key in stages is not a stage ID string
- name if provided in a stage hash is not a string
- folder if provided in a stage hash is not a valid folder path
- input if provided in a stage hash is not a hash or is not valid input for the specified executable
- inputSpecMods or outputSpecMods if provided in a stage hash is not a hash or contains a key which does not abide by the syntax specification above
ResourceNotFound
- The specified workflow does not exist
- One of the specified stage IDs could not be found in the workflow
- A provided input value in an input hash in a stage's hash could not be found
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project

API method: `/workflow-xxxx/isStageCompatible`

Specification

Check whether the proposed replacement executable for a stage is going to be a fully compatible replacement or not.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
stage string ID of the stage to check for compatibility
executable string ID of the executable that would be used as a replacement

Outputs

id string ID of the workflow that was checked for compatibility
compatible boolean The value true if it is compatible and false otherwise

If compatible is false, the following key is also present:

incompatibilities array of strings A list of reasons for which the two executables are not compatible

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- stage is not a string
- executable is not a string
- The given executable is missing an input or output specification
ResourceNotFound
- The specified workflow does not exist
- The specified stage does not exist in the workflow
- The specified executable does not exist
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
PermissionDenied
- User does not have VIEW access to the workflow's project required
- An accessible copy of the executable could not be found

API method: `/workflow-xxxx/updateStageExecutable`

Specification

Update the executable to be run in one of the workflow's stages.

Inputs

editVersion int The edit version number that was last observed, either via /workflow-xxxx/describe or as output from an API call that changed the workflow. This value must match the current version stored in the workflow object for the API call to succeed
stage string ID of the stage to update with the executable
executable string ID of the executable to use for the stage
force boolean (optional, default false) Whether to update the executable even if the one specified in executable is incompatible with the one that is in use for the stage

Outputs

id string ID of the workflow
editVersion int The new edit version number
compatible boolean Whether executable was compatible. If false, then further action (such as setting new inputs) may need to be taken to run the workflow as is

If compatible is false, the following is also present:

incompatibilities list of strings A list of reasons for which the two executables are not compatible

Errors

InvalidInput
- Input is not a hash
- editVersion is not an integer
- stage is not a string, executable is not a string
- The given executable is missing an input or output specification
- force is not a boolean
ResourceNotFound
- The specified workflow does not exist
- The specified stage does not exist in the workflow
- The specified executable does not exist
InvalidState
- Workflow is not in the "open" state
- editVersion provided does not match the current stored value
- The requested executable is not compatible with the previous executable
- force was not set to true
PermissionDenied
- User does not have CONTRIBUTE access to the workflow's project
- An accessible copy of the executable could not be found

API method: `/workflow-xxxx/describe`

Specification

Describes the specified workflow object.

Alternatively, you can use the /system/describeDataObjects method to describe many data objects at once.

Inputs

project string (optional) Project or container ID to be used as a hint for finding an accessible copy of the object
defaultFields boolean (optional, default false if fields is supplied, true otherwise) whether to include the default set of fields in the output (the default fields are described in the "Outputs" section below). The selections are overridden by any fields explicitly named in fields.
fields mapping (optional) include or exclude the specified fields from the output. These selections override the settings in defaultFields.
- key Desired output field. See the "Outputs" section below for valid values here
- value boolean whether to include the field
includeHidden boolean (optional, default false) Whether hidden input and output parameters should appear in the inputSpec and outputSpec fields
getRerunInfo boolean (optional, default false) Whether rerun information should be returned for each stage
rerunStages array of strings (optional) Applicable only if getRerunInfo is set to true. A set of stage IDs that would be forcibly rerun and to return rerun information accordingly
rerunProject string (optional, default is the value of project returned) Project ID to use for retrieving rerun information

The following options are deprecated (and are not respected if fields is present):

properties boolean (optional, default false) Whether the properties should be returned
details boolean (optional, default false) Whether the details should also be returned

Outputs

id string The object ID, such as "workflow-xxxx".

The following fields are included by default (but can be disabled using fields or defaultFields):

project string ID of the project or container in which the object was found
class string The value "workflow"
types array of strings Types associated with the object
created timestamp Time at which this object was created
state string Either "open" or "closed"
hidden boolean Whether the object is hidden or not
links array of strings The object IDs that are pointed to from this object
name string The name of the object
folder string The full path to the folder containing the object
sponsored boolean Whether the object is sponsored by DNAnexus
tags array of strings Tags associated with the object
modified timestamp Time at which the user-provided metadata of the object was last modified
createdBy mapping How the object was created
- user string ID of the user who created the object or launched an execution which created the object
- job string present if a job created the object ID of the job that created the object
- executable string present if a job created the object ID of the app or applet that the job was running
title string The workflow's effective title (always equals name if it has not been set to a string)
summary string The workflow's summary
description string The workflow's description
outputFolder string or null The default output folder for the workflow, or null if unset. See the Customizing Output Folders section above for more details on how it interacts with stages' output folders
inputSpec array of mappings, or null The value is null for inaccessible stage executables. Otherwise, the value is the effective input specification for the workflow. This is generated automatically, taking into account the stages' input specifications and any modifications that have been made to them in the context of the workflow (see the field inputSpecMods under the specification for the /workflow-xxxx/update API method). If not otherwise modified via the API, the group name of an input field is transformed to include a prefix using its stage ID. Hidden parameters are not included unless requested via includeHidden. They have a flag hidden set to true. Bound inputs always show up as default values for the respective input fields.
outputSpec array of mappings, or null The value is null if a stage's executable is inaccessible. Otherwise, the value is effective output specification for the workflow. This is generated automatically, taking into account the stages' output specifications and any modifications that have been made to them in the context of the workflow (see the field outputSpecMods under the specification for the /workflow-xxxx/update API method). Hidden parameters are not included unless requested via includeHidden and they have a flag hidden set to true.
inputs array of mappings, or null Input specification of the workflow (not the input of particular stages, which is returned in inputSpec)
outputs array of mappings, or null Output specification of the workflow (not the output of stages, which is returned in outputSpec)
editVersion int The current edit version of the workflow. This value must be provided with any of the workflow-editing API methods to ensure that simultaneous edits are not occurring
ignoreReuse array of strings, or null Workflow stage ids that are configured to ignore job reuse
stages array of mappings List of metadata for each stage. Each value is a mapping with the key/values:
- id string Stage ID
- executable string App or applet ID
- name string or null Name of the stage or null if not set
- folder string or null The output folder into which outputs should be cloned for the stage. See the Customizing Output Folders section above for more details. null if not set
- input mapping Input (possibly partial) to the stage's executable that has been bound
- accessible boolean Whether the executable is accessible
- executionPolicy mapping The default execution policy for this stage
- systemRequirements mapping The requested systemRequirements value for the stage
- inputSpecMods mapping Modifications for the stage's input parameters when represented in the workflow's input specification
  - key Input parameter name from this stage's executable
  - value mapping Modifications for the input parameter
    name string (present if set) Replacement name of the input parameter. This is guaranteed to be unique in the stages input specification
    label string (present if set) Replacement label for the input parameter
    help string (present if set) Replacement help string for the input parameter
    group string The group to which the input parameter belongs (the empty string indicates no group)
    hidden boolean (present if true) Whether the input field is hidden from the workflow's input specification
- outputSpecMods mapping Modifications for restricting the stages' output and representing its output
  - key Output parameter name from this stage's executable
  - value mapping Modifications for the output parameter with any number of the same key/values that are also present in inputSpecMods. If an output has hidden set to true, its data object value (if applicable) is not cloned into the parent container when the stage or analysis is done and is deleted immediately on completion or failure of the analysis if delayWorkspaceDestruction is not set to true. If getRerunInfo is true, the following keys are present:
- wouldBeRerun boolean Whether the stage would be rerun if the workflow were to be run (taking into account the value given for rerunStages, if applicable)
- cachedExecution string (present if wouldBeRerun is false) The job ID from which the outputs would be used
- cachedOutput mapping or null (present if wouldBeRerun is false) The output from the cached execution if available or null if the execution has not finished yet
- initializedFrom mapping (present if the workflow was created using the initializedFrom option) Basic metadata recording how this workflow was created
- editVersion int (present if id is a workflow ID) The editVersion of the original workflow at the time of creation
- treeTurnaroundTimeThreshold integer or null The turnaround time threshold (in seconds) for trees (specifically, root executions) that run this executable. See Job Notifications for more information about turnaround time and managing job notifications.

A license is required to use the jobNotifications feature. Contact DNAnexus Sales to enable jobNotifications.

The following field (included by default) is available if the object is sponsored by a third party:

sponsoredUntil timestamp Indicates the expiration time of data sponsorship (this field is only set if the object is sponsored, and if set, the specified time is always in the future)

The following fields are only returned if the corresponding field in the fields input is set to true:

properties mapping Properties associated with the object
- key Property name
- value string Property value
details mapping or array Contents of the object's details

Errors

ResourceNotFound
- The specified object does not exist or the specified project does not exist
InvalidInput
- The input is not a hash
- project (if present) is not a string
- The value of properties (if present) is not a boolean
- includeHidden if present is not a boolean
- getRerunInfo if present is not a boolean
- rerunStages if present is not an array of nonempty strings
InvalidType
- rerunProject (if present) is not a project ID
PermissionDenied
- VIEW access is required for the project input if provided
- VIEW access is required for some project containing the specified object, may be different from the project input provided.

API method: `/workflow-xxxx/run`

Specification

All inputs must be provided, either as bound inputs in the workflow or separately in the input field.

Intermediate results are output for the stages and outputs specified.

If any stages have been previously run with the same executable and the same inputs, then the previous results may be used.

Inputs

name string (optional, default is the workflow name) Name for the resulting analysis
input mapping Input for the analysis is launched with
- key Input field name. See the inputSpec and inputs fields in the output of /workflow-xxxx/describe for what the names of the inputs are
- value Input field value
project string (required if invoked by a user. Optional if invoked from a job with detach: true option. Prohibited when invoked from a job with detach: false) The ID of the project in which this workflow runs, also known as the project context. If invoked with the detach: true option, then the detached analysis runs under the provided project (if provided), otherwise project context is inherited from that of the invoking job. If invoked by a user or run as detached, all output objects are cloned into the project context. Otherwise, all output objects are cloned into the temporary workspace of the invoking job. For more information, see The Project Context and Temporary Workspace.

A license is required to launch detached executions. Contact DNAnexus Sales for more information.

folder string (optional) The folder into which objects output by the analysis are placed. If the folder does not exist when the job is complete, the folder is created, along with any parent folders necessary. See the Customizing Output Folders section above for more details on how it interacts with stages' output folders. If no value is provided here and the workflow does not have outputFolder set, then the default value is "/".
stageFolders mapping (optional) Override any stored options for the workflow stages' folder fields. See the Customizing Output Folders section for more details
- key Stage ID or "*" to indicate that the value should be applied to all stages not otherwise mentioned
- value null or string Value to replace the stored default
details array or mapping (optional, default { }) Any conformant JSON, which is defined as a JSON object or array per RFC4627. This is stored with the created job.
delayWorkspaceDestruction boolean (optional) If not given, the value defaults to false for root executions (launched by a user or detached from another job), or to the parent's delayWorkspaceDestruction setting. If set to true, the temporary workspace created for the resulting execution is preserved for 3 days after the job either succeeds or fails.
rerunStages array of strings (optional) A list of stage IDs that should be forcibly rerun. The system automatically identifies stages requiring rerun, and this parameter adds specific stages to that list. If the list includes the string "*", then all stages are rerun
executionPolicy mapping (optional) A collection of options that govern automatic job restart on certain types of failures. This can only be set at the user-level API call (jobs cannot override this for their subjobs). Contents of this field override any of the corresponding keys in the executionPolicy mapping found in individual stages and their executables' run specification (if present). Includes the following optional key/values:
- restartOn mapping (optional) Indicate a job restart policy
  - key A restartable failure reason (ExecutionError, UnresponsiveWorker, JMInternalError, AppInternalError, JobTimeoutExceeded, or SpotInstanceInterruption) or * to indicate all restartable failure reasons that are otherwise not present as keys
  - value int Maximum number of restarts for the failure reason
- maxRestarts int (optional, default 9) Non-negative integer less than 10, indicating the maximum number of times that the job is restarted
- onNonRestartableFailure string (optional) If unset, allows the stages to govern their failure propagation behavior. If set, must be either the value failStage or failAllStages, indicating whether the failure of any stage should propagate failure to all other non-terminal stages in the analysis, even if those stages do not have any dependencies on the failed stage. (Stages that have dependencies on the stage that failed still fail irrespective of this setting)
systemRequirements mapping (optional) Request specific resources for all stages not explicitly specified in stageSystemRequirements. Values are merged with stages' stored values as described in the System Requirements section. See the Requesting Instance Types section for more details
stageSystemRequirements mapping (optional) Request specific resources by stage. Values are merged with stages' stored values as described in the System Requirements section
- key Stage ID
- value mapping Value to override or merge with the stage's systemRequirements value
systemRequirementsByExecutable mapping (optional) Request system requirements for all jobs in the resulting execution tree, configurable by executable and by entry point, described in more detail in the Requesting Instance Types section.
timeoutPolicyByExecutable mapping (optional) The timeout policies for jobs in the resulting job execution tree, configurable by executable and the entry point within that executable. See the timeoutPolicyByExecutable field in /applet-xxxx/run for more details.
allowSSH array of strings (optional, default [ ]) Array of IP addresses or CIDR blocks (up to /16) from which SSH access is allowed to the user by the worker running this job. Array may also include '*' which is interpreted as the IP address of the client issuing this API call as seen by the API server.
debug mapping (optional, default { }) Specify debugging options for running the executable. This field is only accepted when this call is made by a user (and not a job)
- debugOn array of strings (optional, default [ ]) Array of job errors after which the job's worker should be kept running for debugging purposes, offering a chance to SSH into the worker before worker termination (assuming SSH has been enabled). This option applies to all jobs in the execution tree. Jobs in this state for longer than 2 days are automatically terminated but can be terminated earlier. Allowed entries include ExecutionError, AppError, and AppInternalError.
editVersion int (optional) If provided, run the workflow only if the current version matches the provided value and throw an error if it does not match. If not provided, the current version is run.
properties mapping (optional) Properties to associate with the resulting analysis.
- key Property name
- value string Property value
tags array of strings (optional) Tags to associate with the resulting analysis.
singleContext boolean (optional) If true then the resulting jobs and their descendants are only allowed to use the authentication token given to them at the onset. Use of any other authentication token results in an error. This option offers extra security to ensure data cannot leak out of your given context. In restricted projects user-specified value is ignored, and singleContext: true setting is used instead.
ignoreReuse array of strings (optional) Specifies ids of workflow stages (or "*" for all stages) that ignore job reuse. If a specified stage points to a nested sub-workflow, reuse is ignored recursively by the whole nested sub-workflow. Overrides ignoreReuse setting in the workflow and in stage executables.
nonce string (optional) Unique identifier for this request. Ensures that even if multiple requests fail and are retried, only a single analysis is created. For more information, see Nonces.
detach boolean (optional) This option has no impact when the API is invoked by a user. If invoked from a job with detach set to true, the new analysis is detached from the creator job and appears as a typical root execution. A failure in the detached analysis does not cause a termination of the job from which it was created and vice versa. Detached job inherits neither the access to the workspace of its creator job nor the creator job's priority. Detached analysis' access permissions are the intersection (most restricted) of access permissions of the creator job and the permissions requested by jobs' executables in the detached analysis. To launch the detached analysis, creator job must have CONTRIBUTE or higher access to the project in which the detached job is launched. The billTo of the project in which the creator job is running must have a license to launch detached executions.

A license is required to be able to launch detached executions. Contact DNAnexus Sales for more information.

rank integer (optional) An integer between -1024 and 1023, inclusive. The rank indicates the priority in which the executions generated from this executable are processed. The higher the rank, the more prioritized it is. If no rank is provided, the executions default to a rank of zero. If the execution is not a root execution, it inherits its parent's rank. If a rank is provided, all executions relating to the workflow stages also inherit the rank.

A license is required to use the Job Ranking feature. Contact DNAnexus Sales for more information.

costLimit float (optional) The limit of the cost that this execution tree should accrue before termination. This field is ignored if this is not a root execution.
preserveJobOutputs mapping (optional, default is null). Preserves all cloneable outputs of every completed, non-jobReused job in the execution tree launched by this API call in the root execution project, even if root execution ends up failing. Preserving the job outputs in the project trades off higher costs of storage for the possibility of subsequent job reuse.
When a non-jobReused job in the root execution tree launched with non-null preserveJobOutputs enters "done" state, all cloneable objects referenced by the $dnanexus_link in the job's output field are cloned to the project folder described by preserveJobOutputs.folder. This happens unless the output objects already appear elsewhere in the project. Cloneable objects include files, records, applets, and closed workflows, but not databases. If the folder specified by preserveJobOutputs.folder does not exist in the project, the system creates the folder and its parents. As the root job or root analysis' stages complete, the regular outputs of the root execution are moved from preserveJobOutputs.folder to the regular output folders of the root execution. When you run your root execution without the preserveJobOutputs option to completion, some root execution outputs appear in the project in the root execution's output folders. If you had run the same execution with preserveJobOutputs.folder set to "/pjo_folder", the same set of outputs would appear in the same set of root execution folders as in the first case at completion of the root execution. Some additional job outputs that are not outputs of the root execution would appear in "/pjo_folder". preserveJobOutputs argument can be specified only when starting a root execution or a detached job. preserveJobOutputs value, if not null, should be a mapping that may contain the following:
- key "folder" string (optional)
- value path_to_folder string (required if "folder" key is specified). Specifies a folder in the root execution project where the outputs of jobs that are a part of the launched execution are stored. path_to_folder starting with / is interpreted as absolute folder path in the project the job is running in. path_to_folder not starting with / is interpreted as a path relative to the root execution's folder field. An empty string path_to_folder value ("") preserves job outputs in the folder described by root execution's folder field. If the preserveJobOutputs mapping does not have a folder key, the system uses the default folder value of "intermediateJobOutputs". For example, "preserveJobOutputs": {} is equivalent to "preserveJobOutputs": {"folder":"intermediateJobOutputs"}.
  It is recommended to place preserveJobOutputs outputs for different root executions into different folders so as not to create a single folder with a large (>450K) number of files.

A license is required to use preserveJobOutputs. Contact DNAnexus Sales for more information.

detailedJobMetrics boolean Requests detailed metrics collection for jobs if set to true. The default value for this flag is project billTo's detailedJobMetricsCollectDefault policy setting or false if org default is not set. This flag can be specified for root executions and applies to all jobs in the root execution. The list of detailed metrics collected every 60 seconds and viewable for 15 days from the start of a job is available using dx watch --metrics.

A license is required to use detailedJobMetrics. Contact DNAnexus Sales for more information.

Outputs

id string ID of the created analysis object, such as "analysis-xxxx".
stages array of strings List of job IDs that are created for each stage, as ordered in the workflow.

Errors

ResourceNotFound
- The specified workflow object, any referenced apps or applets, or project context does not exist
PermissionDenied
- VIEW access to the workflow, VIEW access to applets, any apps must be installed
- CONTRIBUTE access to the project context required unless called by a job
- When specifying allowSSH or debug options, the user must have developer access to all apps in the workflow, or the apps must have the openSource field set to true
- If preserveJobOutputs is not null and billTo of the project where execution is attempted does not have preserveJobOutputs license.
- detailedJobMetrics setting of true requires project's billTo to have detailedJobMetrics license feature set to true.
- app{let}-xxxx can not run in project-xxxx because executable's httpsApp.shared_access should be NONE to run with isolated browsing.
  - This check applies to all workflow stages.
InvalidInput
- The workflow spec is not complete
- The project context must be in the same region as this workflow
- All data object inputs that are specified directly must be in the same region as the project context.
- All inputs that are job-based object references must refer to a job that was run in the same region as the project context.
- allowSSH accepts only IP addresses or CIDR blocks up to /16
- A nonce was reused in a request but other inputs had changed signifying a new and different request
- A nonce may not exceed 128 bytes
- The billTo of the job's project must be licensed to start detached executions when invoked from the job with detach: true argument
- preserveJobOutputs is specified when launching a non-detached execution from a job.
- preserveJobOutputs.folder value is a syntactically invalid path to a folder.
- detailedJobMetrics can not be specified when launching a non-detached execution from a job.
- timeoutPolicyByExecutable for all executables should not be null
- timeoutPolicyByExecutable for all entry points of all executables should not be null
- timeoutPolicyByExecutable for all entry points of all executables should not exceed 30 days
- Expected key timeoutPolicyByExecutable.* of input to match /^(app|applet)-[0-9A-Za-z]{24}$/
InvalidState
- editVersion was provided and does not match the current sorted value)

For InvalidInput errors that result from a mismatch of an applet or app's input specification, an additional field is provided in the error JSON of the form (see documentation for /applet-xxxx/run for more details.

API method: `/workflow-xxxx/dryRun`

Specification

Perform a dry run of the /workflow-xxxx/run API method.

No new jobs or analyses are created by this method. Any analysis and job IDs returned in the response (except for cached execution IDs) are placeholders and do not represent actual entities in the system.

This method can be used to determine which stages have previous results that would be used. In particular, a stage that would reuse a cached result has a parentAnalysis field (found at stages.N.execution.parentAnalysis where N is the index of the stage) that refers to a preexisting analysis and therefore does not match the top-level field id in the response.

Inputs

Same as would be provided to /workflow-xxxx/run

Outputs

Same as the output if the resulting analysis had been described (see /analysis-xxxx/describe)

Errors

Same as would be thrown if /workflow-xxxx/run had been called with the same input

API method: `/workflow-xxxx/validateBatch`

Specification

This API call verifies that a set of input values for a particular workflow can be used to launch a batch of jobs in parallel.

Batch and common inputs:

batchInput: mapping of inputs corresponding to batches. The value at each position in the array corresponds to the execution of the workflow at that position. Including a null value in an array at a given position means that the corresponding workflow input field is optional and the default value, if defined, should be used. E.g.:

{
  "stage_0.a": [{$dnanexus_link: "file-xxxx"}, {$dnanexus_link: "file-yyyy"}, ....],
  "stage_1.b": [1,null, ...]
}

commonInput: mapping of non-batch, constant inputs common to all batch jobs, e.g.:

{
  "stage_0.c": "foo"
}

File references:

files: list of files (passed as $dnanexus_link references), must be a superset of files included in batchInput and/or commonInput e.g.:

[
  {$dnanexus_link: "file-xxxx"},
  {$dnanexus_link: "file-yyyy"}
]

Output: list of mappings, each mapping corresponds to an expanded batch call. Each mapping contains the input values for the corresponding execution of the workflow, based on its position in the list. E.g.:

[
  {"stage_0.a": {$dnanexus_link: "file-xxxx"}, stage_1.b: 1, stage_0.c: "foo"},
  {"stage_0.a": {$dnanexus_link: "file-yyyy"}, stage_1.b: null, stage_0.c: "foo"}
]

It performs the following validation:

the input types match the expected workflow input field types,
provided inputs are sufficient to run the workflow,
null values are only among values for inputs that are optional or have no specified default values,
all arrays of batchInput are of equal size,
every file referred to in batchInputs exists in files input.

If the workflow is locked, that is, workflow-level inputs are specified for the workflow, this inputs specification is used in place of stage-level inputSpecs, and workflow input field names must be provided in batchInput and commonInput. This happens because for locked workflows input values can only be passed to the workflow-level inputs. For locked workflow we should refer to input fields by their names defined in inputs. To refer to a specific field in a stage of a non-locked workflow, the <stage id>.<input field name defined in inputSpec> format should be used.

Inputs

batchInput mapping Input that the workflow is launched with
- key Input field name. It must be one of the names of the inputs defined in the workflow input specification.
- value Input field values. It must be an array of fields.
commonInput mapping (optional) Input that the workflow is launched with
- key Input field name. It must be one of the names of the inputs defined in the workflow input specification.
- value Input field values. It must be an array of fields.
files list (optional) Files that are needed to run the batch jobs, they must be provided as $dnanexus_links. They must correspond to all the files included in commonInput or batchInput.

Outputs

expandedBatch list of mappings Each mapping contains the input values for one execution of the workflow in batch mode.

Errors

InvalidInput
- Input specification must be specified for the workflow
- Expected batchInput to be a JSON object
- Expected commonInput to be a JSON object
- Expected files to be an array of $dnanexus_link references to files
- The batchInput field is required but empty array was provided
- Expected the value of batchInput for an workflow input field to be an array
- Expected the length of all arrays in batchInput to be equal
- The workflow input field value must be specified in batchInput
- The workflow input field is not defined in the input specification of the workflow
- All the values of a specific batchInput field must be provided (cannot be null) since the field is required and has no default value
- Expected all the files in batchInput and commonInput to be referenced in the files input array

Analysis API Method Specifications

API method: `/analysis-xxxx/describe`

Specification

Describe the specified analysis object.

If the results from previously run jobs are used for any of the stages, they are still listed here. However, the stages' parentAnalysis field still reflects the original analyses in which they were run.

The description of an analysis may not be available if an upstream analysis is not finished running. Users with reorg apps that rely on describing the analysis that is running may want to check the output field dependsOn before the full analysis description becomes available using dx describe analysis-xxx --json | jq -r .dependsOn or equivalent dxpy bindings. The output of the command is an empty array [] if it no longer depends on anything (indicating a status like "done"), which is the signal to proceed. If it contains (sub)analysis IDs, it is not ready, and the reorg script should wait.

Inputs

defaultFields boolean (optional, default false if fields is supplied, true otherwise) Specifies whether to include the default set of fields in the output (the default fields are described in the "Outputs" section below). The selections are overridden by any fields explicitly named in fields.
fields: mapping (optional) include or exclude the specified fields from the output. These selections override the settings in defaultFields.
- key string Desired output field. See the "Outputs" section below for valid values here
- value boolean Whether to include the field

Outputs

id string The object ID, such as "analysis-xxxx".

The following fields are included by default (but can be disabled by setting defaultFields to false or by using the fields input):

class string The value "analysis"
name string Name of the analysis (either specified at creation time or given automatically by the system)
executable string ID of the workflow or the global workflow that was run
executableName string Name of the workflow or the global workflow that was run
created timestamp Time at which this object was created
modified timestamp Time at this analysis was last updated
billTo string ID of the account to which any costs associated with this analysis are billed
project string ID of the project in which this analysis was run
folder string The output folder in which the outputs of this analysis are placed
rootExecution string ID of the job or analysis at the root of the execution tree (the job or analysis created by a user's API call rather than called by a job or as a stage in an analysis)
parentJob string or null ID of the job which created this analysis, or null if this analysis was not created by a job
parentJobTry non-negative integer or null. null is returned if this analysis was not created by a job, or if the parent job had a null try attribute. Otherwise, this analysis was created from the parentJobTry try of the parentJob.
parentAnalysis string or null If this is an analysis that was run as a stage in an analysis, then this is the ID of that analysis. Otherwise, it is null
detachedFrom string or null The ID of the job this analysis was detached from via the detach option, otherwise null
detachedFromTry non-negative integer or null. If this analysis was detached from a job, detachedFrom and detachedFromTry describe the specific try of the job this analysis was detached from. null is returned if this analysis was not detached from another job or if the detachedFrom had a null try attribute
analysis string or null Is null if this analysis was not run as part of a stage in an analysis. Otherwise, the ID of the analysis this analysis is part of
stage string or null Is null if this job was not run as part of a stage in an analysis. Otherwise, the ID of the stage this analysis is part of
workflow mapping Metadata of the workflow that was run, including at least the following fields (analyses created after 8/2014 include the full describe output at the time that the analysis was created):
- id string ID of the workflow
- name string Name of the workflow
- inputs array of mappings Input specification of the workflow
- outputs array of mappings Output specification of the workflow
- stages array of mappings List of metadata for each stage. See description in /workflow-xxxx/describe for more details on what may be returned in each element of the list
- editVersion int Edit version at the time of running the workflow
- initializedFrom mapping If applicable, the initializedFrom mapping from the workflow
stages array of mappings List of metadata for each of the stages' executions
- id string Stage ID
- execution mapping with key id and value of the execution ID. Additional keys are present if the describe hash of the origin job or analysis of the stage has been requested and is available (the fields returned here can be limited by setting fields.stages in the input to the hash one would give to describe the execution)
state string The analysis state, one of in_progress, partially_failed, done, failed, terminating, and terminated
workspace string ID of the temporary workspace assigned to the analysis, such as "container-xxxx".
launchedBy string ID of the user who launched rootExecution. This is propagated to all jobs launched by the analysis
tags array of strings Tags associated with the analysis
properties mapping Properties associated with the analysis
- key Property name
- value string Property value
details array or mapping The JSON details that were stored with this analysis
runInput mapping The value given as input in the API call to run the workflow
originalInput mapping The effective input of the analysis, including all defaults as bound in the stages of the workflow, overridden with any values present in runInput, and all input field names are translated to their canonical names, such as "<stage ID>.<field name>"
input mapping The same as originalInput
output mapping or null Is null if no stages have finished. Otherwise, contains key/value pairs for all outputs that are available (final only when state is one of done, terminated, and failed)
delayWorkspaceDestruction boolean Whether the analysis's temporary workspace is kept around for 3 days after the analysis either succeeds or fails
ignoreReuse array of strings, or null analysis stage ids (or "*" for all stages) that were configured to ignore job reuse.
preserveJobOutputs null or a mapping with preserveJobOutputs.folder expanded to start with "/".
detailedJobMetrics boolean Set to true only if the detailed job metrics collection was enabled for this analysis.
costLimit float If the job is a root execution, and has the root execution cost limit, this is the cost limit for the root execution.
rank int The rank of the analysis, with a range from [-1024 to 1023].

If this job is a root execution, the following fields are included by default (but can be disabled using fields):

selectedTreeTurnaroundTimeThreshold integer or null The selected turnaround time threshold (in seconds) for this root execution. When treeTurnaroundTime reaches the selectedTreeTurnaroundTimeThreshold, the system sends an email about this root execution to the launchedBy user and the billTo profile.
selectedTreeTurnaroundTimeThresholdFrom string or null Where selectedTreeTurnaroundTimeThreshold is from. executable means that selectedTreeTurnaroundTimeThreshold is from this root execution's executable's treeTurnaroundTimeThreshold. system means that selectedTreeTurnaroundTimeThreshold is from the system's default threshold.
treeTurnaroundTime integer The turnaround time (in seconds) of this root execution, which is the time between its creation time and its terminal-state time (or the current time if it is not in a terminal state. Terminal states for an execution include done, terminated, and failed. See Job Lifecyclefor information on them). If this root execution can be retried, the turnaround time begins at the creation time of the root execution's first try, so it includes the turnaround times of all tries.

A license is required to use the jobNotifications feature. Contact DNAnexus Sales to enable jobNotifications.

If the requesting user has permissions to view the pricing model of the billTo of the analysis, and the price for the analysis has been finalized:

currency mapping Information about currency settings, such as dxCode, code, symbol, symbolPosition, decimalSymbol, and groupingSymbol.
totalPrice number Price (in currency) for how much this job (along with all its subjobs) costs.
priceComputedAt timestamp Time at which totalPrice was computed. For billing purposes, the cost of the analysis accrues to the invoice of the month that contains priceComputedAt (in UTC).
totalEgress mapping Egress (in Byte) for how much data amount this job (along with all its subjobs) has egressed.
- regionLocalEgress int Amount in bytes of data transfer between IP in the same cloud region.
- internetEgress int Amount in bytes of data transfer to IP outside of the cloud provider.
- interRegionEgress int Amount in bytes of data transfer to IP in other regions of the cloud provider.
egressComputedAt timestamp Time at which totalEgress was computed. For billing purposes, the cost of the analysis accrues to the invoice of the month that contains egressComputedAt (in UTC).

The following field is only returned if the corresponding field in the fields input is set to true, the requesting user has permissions to view the pricing model of the billTo of the job, and the job is a root execution:

subtotalPriceInfo mapping Information about the current costs associated with all jobs in the tree rooted at this analysis
- subtotalPrice number Current cost (in currency) of the job tree rooted at this analysis
- priceComputedAt timestamp Time at which subtotalPrice was computed
subtotalEgressInfo mapping Information about the aggregated egress amount in bytes associated with all jobs in the tree rooted at this analysis
- subtotalRegionLocalEgress int Amount in bytes of data transfer between IP in the same cloud region.
- subtotalInternetEgress int Amount in bytes of data transfer to IP outside of the cloud provider.
- subtotalInterRegionEgress int Amount in bytes of data transfer to IP in other regions of the cloud provider.
- egressComputedAt timestamp Time at which subtotalEgress was computed

The following fields are returned if the corresponding field in the fields input is set to true:

runSystemRequirements mapping or null A mapping with the systemRequirements values that were passed explicitly to /globalworkflow-xxxx/run or /workflow-xxxx/run when this analysis was created, or null if the systemRequirements input was not supplied the API call that created this analysis.
runStageSystemRequirements mapping or null Similar to runSystemRequirements but for stageSystemRequirements.
runSystemRequirementsByExecutable mapping or null Similar to runSystemRequirements but for systemRequirementsByExecutable.
mergedSystemRequirementsByExecutable mapping or null A mapping with values of systemRequirementsByExecutable supplied to all the ancestors of this analysis and the value supplied to create this analysis, merged as described in the Requesting Instance Types section. If neither the ancestors of this analysis nor this analysis itself were created with the systemRequirementsByExecutable input, mergedSystemRequirementsByExecutable value of null is returned.

Errors

ResourceNotFound
- The specified object does not exist
PermissionDenied
- User does not have VIEW access to the analysis's project context
InvalidInput
- Input is not a hash
- fields (if present) is not a hash or has a non-boolean key (other than stages)
- fields has the key stages and is not a boolean nor a hash

API method: `/analysis-xxxx/addTags`

Specification

Adds the specified tags to the specified analysis. If any of the tags are already present, no action is taken for those tags.

Inputs

tags array of strings Tags to be added

Outputs

id string ID of the manipulated analysis

Errors

InvalidInput
The input is not a hash
The key tags is missing, or its value is not an array, or the array contains at least one invalid (not a string of nonzero length) tag
ResourceNotFound
- The specified analysis does not exist
PermissionDenied
- CONTRIBUTE access is required for the analysis's project context. Otherwise, the request can also be made by jobs sharing the same workspace as the parent job of the specified analysis

API method: `/analysis-xxxx/removeTags`

Specification

Removes the specified tags from the specified analysis. Ensures that the specified tags are not part of the analysis -- if any of the tags are already missing, no action is taken for those tags.

Inputs

tags array of strings Tags to be removed

Outputs

id string ID of the manipulated analysis

Errors

InvalidInput
- The input is not a hash
- The key tags is missing, or its value is not an array, or the array contains at least one invalid (not a string of nonzero length) tag
ResourceNotFound
- The specified analysis does not exist
PermissionDenied
- CONTRIBUTE access is required for the analysis's project context. Otherwise, the request can also be made by jobs sharing the same workspace as the parent job of the specified analysis

API method: `/analysis-xxxx/setProperties`

Specification

Sets properties on the specified analysis. To remove a property altogether, its value needs to be set to the JSON null (instead of a string). This call updates the properties of the analysis by merging any old (previously existing) ones with what is provided in the input, the newer ones taking precedence when the same key appears in the old.

To reset properties, you need to remove all existing key/value pairs and replace them with new ones. First, issue a describe call to get the names of all properties. Then issue a setProperties request to set the values of those properties to null.

Inputs

properties mapping Properties to modify
- key Name of property to modify
- value string or null Either a new string value for the property, or null to unset the property

Outputs

id string ID of the manipulated analysis

Errors

InvalidInput
- There exists at least one value in properties which is neither a string nor the JSON null
- For each property key-value pair, the size, encoded in UTF-8, of the property key may not exceed 100 bytes and the property value may not exceed 700 bytes
ResourceNotFound
- The specified analysis does not exist
PermissionDenied
- CONTRIBUTE access is required for the analysis's project context. Otherwise, the request can also be made by jobs sharing the same workspace as the parent job of the specified analysis

API method: `/analysis-xxxx/terminate`

Specification

Terminates an analysis and the stages' origin jobs and/or analyses. This call is only valid from outside the platform.

Analyses can only be terminated by the user who launched the analysis and has at least CONTRIBUTE access or by any user with ADMINISTER access to the project context.

Inputs

None

Outputs

id string ID of the terminated analysis, such as "analysis-xxxx".

Errors

ResourceNotFound
- The specified object does not exist
PermissionDenied
- ADMINISTER access required to the project context of the job or else the user must match the launchedBy entry of the analysis object
InvalidState
- The analysis is not in a state from which it can be terminated, for example, it is in a terminal state

API method: `/analysis-xxxx/update`

Specification

Updates an analysis and its stages' jobs and/or analyses. This call is only valid from outside the platform. You can only update the rank of root analyses.

A valid rank field must be provided. To update rank, the organization associated with this analysis must have the license feature executionRankEnabled active. The user must also be either the original launcher of the analysis or an administrator of the organization.

When supplying rank, the job or analysis being updated must be a rootExecution, and must be in a state capable of creating more jobs. rank cannot be supplied for terminal states like terminated, done, failed, or debug_hold.

Inputs

rank integer The rank to set the analysis and its children executions to.

A license is required to use the Job Ranking feature. Contact DNAnexus Sales for more information.

Outputs

id string ID of the updated analysis, such as "analysis-xxxx".

Errors

InvalidInput
- Input is not a hash
- Expected input to have property rank
- Expected key rank of input to be an integer
- Expected key rank of input to be in range [-1024, 1023]
- Not a root execution
PermissionDenied
- billTo does not have license feature executionRankEnabled
- Not permitted to change rank
ResourceNotFound
- The specified object does not exist

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Editing a Workflow

Managing Stages

Stage ID and Name

Customizing Output Folders

Stage Output Folders

Workflow Input and Output (Locked Workflows)

Workflow Input

Workflow Output

Binding Input

Linking input to other stage output

Linking input to other stage input

Linking workflow input to stage input

Customizing IO Specifications

Execution Policy

System Requirements

Reuse of Previous Results

Analysis Input

Workflow API Method Specifications

API method: /workflow/new

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/overwrite

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/addStage

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/removeStage

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/moveStage

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/update

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/isStageCompatible

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/updateStageExecutable

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/describe

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/run

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/dryRun

Specification

Inputs

Outputs

Errors

API method: /workflow-xxxx/validateBatch

Specification

Inputs

Outputs

Errors

Analysis API Method Specifications

API method: /analysis-xxxx/describe

API method: `/workflow/new`

API method: `/workflow-xxxx/overwrite`

API method: `/workflow-xxxx/addStage`

API method: `/workflow-xxxx/removeStage`

API method: `/workflow-xxxx/moveStage`

API method: `/workflow-xxxx/update`

API method: `/workflow-xxxx/isStageCompatible`

API method: `/workflow-xxxx/updateStageExecutable`

API method: `/workflow-xxxx/describe`

API method: `/workflow-xxxx/run`

API method: `/workflow-xxxx/dryRun`

API method: `/workflow-xxxx/validateBatch`

API method: `/analysis-xxxx/describe`

API method: `/analysis-xxxx/addTags`

API method: `/analysis-xxxx/removeTags`

API method: `/analysis-xxxx/setProperties`

API method: `/analysis-xxxx/terminate`

API method: `/analysis-xxxx/update`