project_id or project

integer or string

A project specification

owner

string

Sets the project owner

name

string

Sets the project name

description

string

Sets the project description

collaborator

string

If this parameter is specified, then “role” must also be specified. If the role parameter is “remove” then the specified collaborator is removed from the project, otherwise role must be a valid project role (Collaborator or Viewer).

my_output_folder

string

Sets the project output folder for the user making the request

output_folder

string

Sets the project output folder for all collaborators the user making the request has permission to affect

project_id or project

integer or string

A project specification

project_id or project

integer or string

A project specification

message

String

project_ids

comma-delimited integers

A specification for one or more projects

includeLibraryFiles

boolean

If equal to true then library files will be included

outputFolder

String

A path on the server to write the exported projects to.

Stream the project(s) to the requestor

project_ids

string

Retrieve specific projects. IDs joined by ,

project_id

integer

Retrieve a single project by ID

project

string

Retrieve a single project by name

sample

string

List projects that contain a sample with the specified name

file_name

string

List projects that contain a file matching the specified sub-string

user_id

integer

List projects for which the specified user is a member

user_name

string

List projects for which the specified user is a member

url or filepath or file

string or string or binary

The location of a project zip: on a remote server or on the specified server or in the stream

owner_id or owner_name

integer or string

This user will be the owner of the imported project

By default, the user making the API request will be the owner

project_ids

string

Retrieve specific projects. IDs joined by ,

project_id

integer

Retrieve a single project by ID

project

string

Retrieve a single project by name

sample

string

List projects that contain a sample with the specified name

file_name

string

List projects that contain a file matching the specified sub-string

user_id

integer

List projects for which the specified user is a member

user_name

string

List projects for which the specified user is a member

project_ids

string

Retrieve specific projects. IDs joined by ,

project_id

integer

Retrieve a single project by ID

project

string

Retrieve a single project by name

sample

string

List projects that contain a sample with the specified name

file_name

string

List projects that contain a file matching the specified sub-string

user_id

integer

List projects for which the specified user is a member

user_name

string

List projects for which the specified user is a member

key

String

The name of the property

value

String

The value of the property

project_id or project

integer or string

A project specification

project_id or project

integer or string

A project specification

project_ids

string

Retrieve specific projects. IDs joined by ,

project_id

integer

Retrieve a single project by ID

project

string

Retrieve a single project by name

sample

string

List projects that contain a sample with the specified name

file_name

string

List projects that contain a file matching the specified sub-string

user_id

integer

List projects for which the specified user is a member

user_name

string

List projects for which the specified user is a member

project_id

integer

importing

String

attribute_json

String

A set of attributes in the same format as returned by /samples/attributes

attribute_txt

String

A set of attributes in a tab-delimited file

sample_id or sample_name

integer or string

A sample specification

(attribute or numeric_attribute) and value

String

project_id or project

integer or string

A project specification

sample_id or sample_name

integer or string

A sample specification

project_id or project

integer or string

A project specification

project_id or project

integer or string

A project specification

filepath and/or filepath1 and/or filepath2

String

The location of the file on the server. Up to three files can by imported at once.

sample_id or sample or new_sample

integer string string

The id or name of the sample to add data to. If new_sample is specified and the sample already exists characters will be added to disambiguate the new sample

owner

string

The username of the user that should be the owner of the data. The data will count against this user’s quota, if one is configured.

The owner will be the user account that uploads the data

upload_folder

string

If the file is uploaded through the servlet it will be put in this directory, if the owner has permission to access it.

resource_id

integer

A resource ID

resource_id

integer

A resource ID

directory

String

former

String

Old path to the data

current

String

New path to the data

task_id

integer

The ID of the task that produced the table

table

String

The table to download, if ambiguous for the task.
QuantificationSummary, TranscriptQuantificationSummary, GeneQuantificationSummary, transcript_feature_distribution, gene_feature_distribution

QuantificationSummary

directory

String

file or filepath

binary or string

The file content or the path of the file on the server

file_type

String

The type of library file. The list of available library file types is returned by /library_files/types

assembly

String

The assembly of the library file

species

string

The species of the library file. This is looked up based on the assembly, and the assembly is used as the species if the assembly is not associated with any species

file_type

String

Filters results based on file type

annotation_model

String

Filters results based on annotation model

descriptions

String

Filters results based on the description

id

String

Return a result for a specific library file

genome_build

String

database

String

pipeline

String

The name of the pipeline

pipeline

String

The name of the pipeline

project_id or project

integer or string

A project specification

data

String

The data node that the pipeline will run on, as returned by the /projects interface.

Unaligned reads

pipeline

String

The name of the pipeline

project_id or project

integer or string

A project specification

inputs

integers

The ids of the resources, in the order returned by the /pipeline/inputs interface. The ids of library files are returned by the /library_files interface.

data

String

The data node that the pipeline will run on, as returned by the /projects interface.

Unaligned reads

project or project_name or project_filter

string

Only return tasks in this project

project_id

integer

Only return tasks in this project

user_name or user_filter

string

Only return tasks run by this user

user_id

integer

Only return tasks run by this user

status

string

Only return tasks matching this status

project or project_name or project_filter

string

Only return tasks in this project

project_id

integer

Only return tasks in this project

user_name or user_filter

string

Only return tasks run by this user

user_id

integer

Only return tasks run by this user

status

string

Only return tasks matching this status

project or project_name or project_filter

string

Only return tasks in this project

project_id

integer

Only return tasks in this project

user_name or user_filter

string

Only return tasks run by this user

user_id

integer

Only return tasks run by this user

status

string

Only return tasks matching this status

user_id or user_name

integer or string

A user specification. If user_name is specified the account will be created if it does not already exist

If this is not specified, the configuration will apply to the user making the request

distinguished_name

string

When creating a new user, this parameter specifies the LDAP distinguished name.

user_password

string

When creating a new user, this parameter specifies their initial Flow password. If this parameter is absent and this is not an LDAP user then the user will receive an email with a link to set their initial password.

email

string

The user’s email address. When creating a new user, this parameter is required.

display_name

string

The name that other users will see.

enabled

boolean

Whether the user is able to log in

add_role_name or add_role_id

string or integer

Add the user to the specified role

remove_role_name or remove_role_id

string or integer

Remove the user from the specified role

private_directory

string

If present, the directory will be created and the user will be given permission to use it.

add_directory

string

Add permission for the user to browse files in this directory.

quota

integer

The size of the user’s quota (in gigabytes) or “none” to remove any quota

notify_when_tasks_finish

boolean

Whether the user will receive an email when a task they have queued completes

notify_when_added_to_project

boolean

Whether the user will receive an email when they are added as a collaborator or viewer to a project

decimal_precision

integer

How many digits to show after the decimal point for numeric values in tables

user_id or user_name

integer or string

A user specification.

If this is not specified, the user making the request will be used

key

String

The name of the preference

value

String

The value of the preference

user_id or user_name

integer or string

A user specification.

If this is not specified, the user making the request will be used

enforce

boolean

directory

String

user_id or user_name or group_id or group_name

integer or string or integer or string

A member specification

If a user or group is not specified, this action will apply to all users

directory

String

user_id or user_name or group_id or group_name

integer or string or integer or string

A member specification

If a user or group is not specified, this action will apply to all users

id

integer

keep_output

boolean

false

project_id or project

integer or string

A project specification

id

integer

A single task ID

user_name or user_id

string or integer

The username or ID of a user that has run tasks

status

String

A task status: Pending, Waiting, Running, Done, Canceled, Failed

task

String

A sub-string of the task name & version as it appears in the Task entry on the task details page

project_id or project

integer or string

A project specification

id

integer

A single task ID

user_name or user_id

string or integer

The username or ID of a user that has run tasks

status

String

A task status: Pending, Waiting, Running, Done, Canceled, Failed

task

String

A sub-string of the task name & version as it appears in the Task entry on the task details page

filepath or filter

String

filepath: a file on the server with filter content or filter: the filter content in json format

task

integer

Filter commands to those belonging to the specified task ID

worker_identifier

integer

Filter commands to those run on the specified worker

successful

boolean

Filter commands based on whether they successfully completed

command_line

String

Filter commands based on their command-line representation

id

String

A specific command identifier

task

integer

Filter results based on a task ID

command

String

Filter results based on the command

conservative

boolean

Include/exclude results based on whether they are flagged as conservative

feature

String

Filters results based on feature name

submitted_workers

integer

max_memory_mb

integer

page_load_log_threshold

integer

If specified and greater than 0 a warning will be written to logs/page_load.log whenever a page-load takes longer than this value (in seconds)

expiration

String

never for no expiration, otherwise: d-M-yyyy h:mm a

duration

integer

duration of the token, in hours

1 hour

logger

string

The name of a logger or "commands" to configure multiple command-related logs.

log_level

string

Sets the level of the specified logger: ALL, TRACE, DEBUG, INFO, WARN, ERROR, OFF

node

String

Required unless deleting from the root node

key

String

The ID of the preference to delete

node

string

The node name

key

string

The preference name

value

string

The preference value

api_key

String

An API token to revoke. "mine" to revoke the requestors tokens, "all" to revoke all managed tokens (requires Change user accounts privilege)

api_key

String

The token to configure

Return a list of all tokens managed for the requestor

expiration

String

never for no expiration, otherwise: d-M-yyyy h:mm a