Command Index

The build number, together with the used libraries and licenses are provided in the accompanying readme file.

icav2

Command line interface for the Illumina Connected Analytics, a genomics platform-as-a-service

Usage:
  icav2 [command]

Available Commands:
  analysisstorages      Analysis storages commands
  completion            Generate the autocompletion script for the specified shell
  config                Config actions
  dataformats           Data format commands
  help                  Help about any command
  jobs                  Job commands
  metadatamodels        Metadata model commands
  pipelines             Pipeline commands
  projectanalyses       Project analyses commands
  projectdata           Project Data commands
  projectpipelines      Project pipeline commands
  projects              Project commands
  projectsamples        Project samples commands
  regions               Region commands
  storagebundles        Storage bundle commands
  storageconfigurations Storage configurations commands
  tokens                Tokens commands
  version               The version of this application

Flags:
  -t, --access-token string    JWT used to call rest service
  -h, --help                   help for icav2
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -v, --version                version for icav2
  -k, --x-api-key string       api key used to call rest service

Use "icav2 [command] --help" for more information about a command.

icav2 analysisstorages

This is the root command for actions that act on analysis storages

Usage:
  icav2 analysisstorages [command]

Available Commands:
  list        list of storage id's

Flags:
  -h, --help   help for analysisstorages

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 analysisstorages [command] --help" for more information about a command.

icav2 analysisstorages list

This command lists all the analysis storage id's

Usage:
  icav2 analysisstorages list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion

This command generates custom completion functions for icav2 tool. These functions facilitate the generation of context-aware suggestions based on the user's input and specific directives provided by the icav2 tool. For example, for ZSH shell the completion function _icav2() is generated. It could provide suggestions for available commands, flags, and arguments depending on the context, making it easier for the user to interact with the tool without having to constantly refer to documentation.

To enable this custom completion function, you would typically include it in your Zsh configuration (e.g., in .zshrc or a separate completion script) and then use the compdef command to associate the function with the icav2 command:

compdef _icav2 icav2

This way, when the user types icav2 followed by a space and presses the TAB key, Zsh will call the _icav2 function to provide context-aware suggestions based on the user's input and the icav2 tool's directives.

Generate the autocompletion script for icav2 for the specified shell.
See each sub-command's help for details on how to use the generated script.

Usage:
  icav2 completion [command]

Available Commands:
  bash        Generate the autocompletion script for bash
  fish        Generate the autocompletion script for fish
  powershell  Generate the autocompletion script for powershell
  zsh         Generate the autocompletion script for zsh

Flags:
  -h, --help   help for completion

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 completion [command] --help" for more information about a command.

icav2 completion bash

Generate the autocompletion script for the bash shell.

This script depends on the 'bash-completion' package.
If it is not installed already, you can install it via your OS's package manager.

To load completions in your current shell session:

	source <(icav2 completion bash)

To load completions for every new session, execute once:

#### Linux:

	icav2 completion bash > /etc/bash_completion.d/icav2

#### macOS:

	icav2 completion bash > $(brew --prefix)/etc/bash_completion.d/icav2

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion bash

Flags:
  -h, --help              help for bash
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion fish

Generate the autocompletion script for the fish shell.

To load completions in your current shell session:

	icav2 completion fish | source

To load completions for every new session, execute once:

	icav2 completion fish > ~/.config/fish/completions/icav2.fish

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion fish [flags]

Flags:
  -h, --help              help for fish
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion powershell

Generate the autocompletion script for powershell.

To load completions in your current shell session:

	icav2 completion powershell | Out-String | Invoke-Expression

To load completions for every new session, add the output of the above command
to your powershell profile.

Usage:
  icav2 completion powershell [flags]

Flags:
  -h, --help              help for powershell
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion zsh

Generate the autocompletion script for the zsh shell.

If shell completion is not already enabled in your environment you will need
to enable it.  You can execute the following once:

	echo "autoload -U compinit; compinit" >> ~/.zshrc

To load completions in your current shell session:

	source <(icav2 completion zsh)

To load completions for every new session, execute once:

#### Linux:

	icav2 completion zsh > "${fpath[1]}/_icav2"

#### macOS:

	icav2 completion zsh > $(brew --prefix)/share/zsh/site-functions/_icav2

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion zsh [flags]

Flags:
  -h, --help              help for zsh
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 config

Config command provides functions for CLI configuration management.

Usage:
  icav2 config [command]

Available Commands:
  get         Get configuration information
  reset       Remove the configuration information
  set         Set configuration information

Flags:
  -h, --help   help for config

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 config [command] --help" for more information about a command.

icav2 config get

Get configuration information.

Usage:
  icav2 config get [flags]

Flags:
  -h, --help   help for get

icav2 config reset

Remove configuration information.

Usage:
  icav2 config reset [flags]

Flags:
  -h, --help   help for reset

icav2 config set

Set configuration information. Following information is asked when starting the command : 

 - server-url : used to form the url for the rest api's. 
 - x-api-key : api key used to fetch the JWT used to authenticate to the API server. 
 - colormode : set depending on your background color of your terminal. Input's and errors are colored. Default is 'none', meaning that no colors will be used in the output.
 - table-format : Output layout, defaults to a table, other allowed values are json and yaml

Usage:
  icav2 config set [flags]

Flags:
  -h, --help   help for set

icav2 dataformats

This is the root command for actions that act on Data formats

Usage:
  icav2 dataformats [command]

Available Commands:
  list        List data formats

Flags:
  -h, --help   help for dataformats

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 dataformats [command] --help" for more information about a command.

icav2 dataformats list

This command lists the data formats you can use inside of a project

Usage:
  icav2 dataformats list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 help

Help provides help for any command in the application.
Simply type icav2 help [path to command] for full details.

Usage:
  icav2 help [command] [flags]

Flags:
  -h, --help   help for help

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 jobs

This is the root command for actions that act on jobs

Usage:
  icav2 jobs [command]

Available Commands:
  get         Get details of a job

Flags:
  -h, --help   help for jobs

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 jobs [command] --help" for more information about a command.

icav2 jobs get

This command fetches the details of a job using the argument as an id (uuid).

Usage:
  icav2 jobs get [job id] [flags]

Flags:
  -h, --help   help for get

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 metadatamodels

This is the root command for actions that act on metadata models

Usage:
  icav2 metadatamodels [command]

Available Commands:
  list        list of metadata models

Flags:
  -h, --help   help for metadatamodels

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 metadatamodels [command] --help" for more information about a command.

icav2 metadatamodels list

This command lists all the metadata models

Usage:
  icav2 metadatamodels list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 pipelines

This is the root command for actions that act on pipelines

Usage:
  icav2 pipelines [command]

Available Commands:
  get         Get details of a pipeline
  list        List pipelines

Flags:
  -h, --help   help for pipelines

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 pipelines [command] --help" for more information about a command.

icav2 pipelines get

This command fetches the details of a pipeline without a project context

Usage:
  icav2 pipelines get [pipeline id] [flags]

Flags:
  -h, --help   help for get

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 pipelines list

This command lists the pipelines without the context of a project

Usage:
  icav2 pipelines list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses

This is the root command for actions that act on projects analysis

Usage:
  icav2 projectanalyses [command]

Available Commands:
  get         Get the details of an analysis 
  input       Retrieve input of analyses commands
  list        List of analyses for a project 
  output      Retrieve output of analyses commands
  update      Update tags of analyses

Flags:
  -h, --help   help for projectanalyses

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectanalyses [command] --help" for more information about a command.

icav2 projectanalyses get

This command returns all the details of a analysis.

Usage:
  icav2 projectanalyses get [analysis id] [flags]

Flags:
  -h, --help                help for get
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses input

Retrieve input of analyses commands

Usage:
  icav2 projectanalyses input [analysisId] [flags]

Flags:
  -h, --help                help for input
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses list

This command lists the analyses for a given project. Sorting can be done on 
- reference
- userReference
- pipeline
- status
- startDate
- endDate
- summary

Usage:
  icav2 projectanalyses list [flags]

Flags:
  -h, --help                help for list
      --max-items int       maximum number of items to return, the limit and default is 1000
      --page-offset int     Page offset, only used in combination with sort-by. Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages
      --page-size int32     Page size, only used in combination with sort-by. The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --project-id string   project ID to set current project context
      --sort-by string      specifies the order to list items

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses output

Retrieve output of analyses commands

Usage:
  icav2 projectanalyses output [analysisId] [flags]

Flags:
  -h, --help                help for output
      --project-id string   project ID to set current project context
      --raw-output          Add this flag if output should be in raw format. Applies only for Cwl pipelines ! This flag needs no value, adding it sets the value to true.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses update

Updates the user and technical tags of an analysis

Usage:
  icav2 projectanalyses update [analysisId] [flags]

Flags:
      --add-tech-tag stringArray      Tech tag to add to analysis. Add flag multiple times for multiple values.
      --add-user-tag stringArray      User tag to add to analysis. Add flag multiple times for multiple values.
  -h, --help                          help for update
      --project-id string             project ID to set current project context
      --remove-tech-tag stringArray   Tech tag to remove from analysis. Add flag multiple times for multiple values.
      --remove-user-tag stringArray   User tag to remove from analysis. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata

This is the root command for actions that act on projects data

Usage:
  icav2 projectdata [command]

Available Commands:
  archive              archive data 
  copy                 Copy data to a project
  create               Create data id for a project
  delete               delete data 
  download             Download a file/folder
  downloadurl          get download url 
  folderuploadsession  Get details of a folder upload
  get                  Get details of a data
  link                 Link data to a project
  list                 List data 
  mount                Mount project data 
  move                 Move data to a project
  temporarycredentials fetch temporal credentials for data
  unarchive            unarchive data 
  unlink               Unlink data to a project
  unmount              Unmount project data 
  update               Updates the details of a data
  upload               Upload a file/folder

Flags:
  -h, --help   help for projectdata

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectdata [command] --help" for more information about a command.

icav2 projectdata archive

This command archives data for a given project

Usage:
  icav2 projectdata archive [path or data Id] [flags]

Flags:
  -h, --help                help for archive
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata copy

This command copies data between projects. Use data id or a combination of path and --source-project-id to identify the source data. By default, the root folder of your current project will be used as destination. If you want to specify a destination, use --destination-folder to specify the destination path or folder id.

Usage:
  icav2 projectdata copy [data id] or [path] [flags]

Flags:
      --action-on-exist string      what to do when a file or folder with the same name already exists: OVERWRITE|SKIP|RENAME (default "SKIP")
      --background                  starts job in background on server. Does not provide upload progress updates. Use icav2 jobs get with the current job.id value
      --copy-instrument-info        copy instrument info form source data to destination data
      --copy-technical-tags         copy technical tags form source data to destination data
      --copy-user-tags              copy user tags form source data to destination data
      --destination-folder string   folder id or path to where you want to copy the data, default root of project
  -h, --help                        help for copy
      --polling-interval int        polling interval in seconds for job status, values lower than 30 will be set to 30 (default 30)
      --project-id string           project ID to set current project context
      --source-project-id string    project ID from where the data needs to be copied, mandatory when using source path notation

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata create

This command creates a data on a project. It takes name of file/folder as an argument

Usage:
  icav2 projectdata create [name] [flags]

Flags:
      --data-type string     (*) Data type : FILE or FOLDER
      --folder-id string     Id of the folder
      --folder-path string   Folder path under which the new project data will be created.
      --format string        Only allowed for file, sets the format of the file.
  -h, --help                 help for create
      --project-id string    project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata delete

This command deletes data for a given project

Usage:
  icav2 projectdata delete [path or dataId] [flags]

Flags:
  -h, --help                help for delete
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata download

Download a file/folder.  Source path can be a data id or a path. Source path for download of a folder should end with '*'. For files : Target defines either local folder into which the download will occur, or a path with a new name for the file. If the  file already exists locally, it is overwritten. For folders : If folder does not exist locally, it will be created automatically. Overwrite of an existing folder will need to be acknowledged.

Usage:
  icav2 projectdata download [source data id or path] [target path] [flags]

Flags:
      --exclude string        Regex filter for file names to exclude from download.
      --exclude-source-path   Indicates that on folder download, the CLI will not create the parent folders of the downloaded folder in ICA on your local machine.
  -h, --help                  help for download
      --project-id string     project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Example 1

Using this command all the files starting with VariantCaller- will be downloaded (prerequisite: a tool jq is installed on the machine):

icav2 projectdata list --data-type FILE --file-name VariantCaller- --match-mode FUZZY -o json | jq -r '.items[].id' > filelist.txt; for item in $(cat filelist.txt); do echo "--- $item ---"; icav2 projectdata download $item . ; done;

Example 2

Here an example of how to download all BAM files from a project (we are using some jq features to remove '.bam.bai' and '.bam.md5sum' files)

icav2 projectdata list --file-name .bam --match-mode FUZZY -o json | jq -r '.items[] | select(.details.format.code == "BAM") | [.id] | @tsv' > filelist.txt; for item in $(cat filelist.txt); do echo "--- $item ---"; icav2 projectdata download $item . ; done

Tip: If you want to look up a file id from the GUI, go to that file and open te details view. The file id can be found on the top left side and will begin with fil.

icav2 projectdata downloadurl

This command returns the data download url for a given project

Usage:
  icav2 projectdata downloadurl [path or data Id] [flags]

Flags:
  -h, --help                help for downloadurl
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata folderuploadsession

This command fetches the details a folder upload

Usage:
  icav2 projectdata folderuploadsession [project id] [data id] [folder upload session id] [flags]

Flags:
  -h, --help                help for folderuploadsession
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata get

This command fetches the details a data

Usage:
  icav2 projectdata get [data id] or [path] [flags]

Flags:
  -h, --help                help for get
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata link

This links data to a project. Use data id or the path + the source project flag identify the data.

Usage:
  icav2 projectdata link [data id] or [path] [flags]

Flags:
  -h, --help                       help for link
      --project-id string          project ID to set current project context
      --source-project-id string   project ID from where the data needs to be linked

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata list

It is best practice to always surround your path with quotes if you want to use the * wildcard. Otherwise, you may run into situations where the command results in "accepts at most 1 arg(s), received x" as it returns folders with the same name, but different amounts of subfolders.

For more information on how to use pagination, please refer to Cursor- versus Offset-based Pagination

If you want to look up a file id from the GUI, go to that file and open te details view. The file id can be found on the top left side and will begin with fil.

This command lists the data for a given project. Page-offset can only be used in combination with sort-by. Sorting can be done on 
- timeCreated
- timeModified
- name
- path
- fileSizeInBytes
- status
- format
- dataType
- willBeArchivedAt
- willBeDeletedAt

Usage:
  icav2 projectdata list [path] [flags]

Flags:
      --data-type string        Data type. Available values : FILE or FOLDER
      --eligible-link           Add this flag if output should contain only the data that is eligible for linking on the current project. This flag needs no value, adding it sets the value to true.
      --file-name stringArray   The filenames to filter on. The filenameMatchMode-parameter determines how the filtering is done. Add flag multiple times for multiple values.
  -h, --help                    help for list
      --match-mode string       Match mode for the file name. Available values : EXACT (default), EXCLUDE, FUZZY.
      --max-items int           maximum number of items to return, the limit and default is 1000
      --page-offset int         Page offset, only used in combination with sort-by. Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages
      --page-size int32         Page size, only used in combination with sort-by. The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --parent-folder           Indicates that the given argument is path of the parent folder. All children are selected for list, not the folder itself. This flag needs no value, adding it sets the value to true.
      --project-id string       project ID to set current project context
      --sort-by string          specifies the order to list items
      --status stringArray      Add the status of the data. Available values : PARTIAL, AVAILABLE, ARCHIVING, ARCHIVED, UNARCHIVING, DELETING. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Example to list files in the folder SOURCE

icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/

Example to list only subfolders in the folder SOURCE

icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/ --data-type FOLDER

icav2 projectdata mount

This command mounts the project data as a file system directory for a given project

Usage:
  icav2 projectdata mount [mount directory path] [flags]

Flags:
      --allow-other         Allow other users to access this project
  -h, --help                help for mount
      --list                List currently mounted projects
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata move

This command moves data between projects. Use data id or a combination of path and --source-project-id to identify the source data. By default, the root folder of your current project will be used as destination. If you want to specify a destination, use --destination-folder to specify the destination path or folder id.

Usage:
  icav2 projectdata move [data id] or [path] [flags]

Flags:
      --background                  starts job in background on server. Does not provide upload progress updates. Use icav2 jobs get with the current job.id value
      --destination-folder string   folder id or path to where you want to move the data, default root of project
  -h, --help                        help for move
      --polling-interval int        polling interval in seconds for job status, values lower than 30 will be set to 30 (default 30)
      --project-id string           project ID to set current project context
      --source-project-id string    project ID from where the data needs to be moved, mandatory when using source path notation

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata temporarycredentials

This command fetches  temporal AWS and Rclone credentials for a given project-data. If path is given, project id from the flag --project-id is used. If flag not present project is taken from the context

Usage:
  icav2 projectdata temporarycredentials [path or data Id] [flags]

Flags:
  -h, --help                help for temporarycredentials
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata unarchive

This command unarchives data for a given project

Usage:
  icav2 projectdata unarchive [path or dataId] [flags]

Flags:
  -h, --help                help for unarchive
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata unlink

This unlinks data from a project. Use path or id to identifiy the data.

Usage:
  icav2 projectdata unlink [data id] or [path] [flags]

Flags:
  -h, --help                help for unlink
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata unmount

This command unmounts previously mounted project data

Usage:
  icav2 projectdata unmount [flags]

Flags:
      --directory-path string   Set path to unmount
  -h, --help                    help for unmount
      --project-id string       project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata update

This command updates some details of a data. Only user/tech tags, format and dates of will be archived/delete can be updated.

Usage:
  icav2 projectdata update [data id] or [path] [flags]

Flags:
      --add-tech-tag stringArray      Tech tag to add. Add flag multiple times for multiple values.
      --add-user-tag stringArray      User tag to add. Add flag multiple times for multiple values.
      --format-code string            Format to assign to the data. Only available for files.
  -h, --help                          help for update
      --project-id string             project ID to set current project context
      --remove-tech-tag stringArray   Tech tag to remove. Add flag multiple times for multiple values.
      --remove-user-tag stringArray   User tag to remove. Add flag multiple times for multiple values.
      --will-be-archived-at string    Time when data will be archived. Format is YYYY-MM-DD. Time is set to 00:00:00UTC time. Only available for files.
      --will-be-deleted-at string     Time when data will be deleted. Format is YYYY-MM-DD. Time is set to 00:00:00UTC time. Only available for files.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata upload

Upload a file/folder.  For files : if the target path does not already exist, it will be created automatically. For folders : overwrite will need to be acknowledged. Argument "icapath" is optional.

Usage:
  icav2 projectdata upload [local path] [icapath] [flags]

Flags:
      --existing-sample                    Link to existing sample
  -h, --help                               help for upload
      --new-sample                         Create and link to new sample
      --num-workers int                    number of workers to parallelize.  Default calculated based on CPUs available.
      --project-id string                  project ID to set current project context
      --sample-description string          Set Sample Description for new sample
      --sample-id string                   Set Sample id of existing sample
      --sample-name string                 Set Sample name for new sample or from existing sample
      --sample-technical-tag stringArray   Set Sample Technical tag for new sample
      --sample-user-tag stringArray        Set Sample User tag for new sample

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Example for uploading multiple files

In this example all the fastq.gz files from source will be uploaded to target using xargs utility.

find $source -name '*.fastq.gz' | xargs -n 1 -P 10 -I {} icav2 projectdata upload {} /$target/

Example for uploading multiple files using a CSV file

In this example we upload multiple bam files specified with the corresponding path in the file bam_files.csv. The files will be renamed. We are using screen in detached mode (this creates a new session but not attaching to it):

while IFS=, read -r current_bam_file_name bam_path new_bam_file_name
do
screen -d -m icav2 projectdata upload ${bam_path}/${current_bam_file} /bam_files/${new_bam_file_name} --project-id $projectID
done <./bam_files.csv 2>./log.txt

icav2 projectpipelines

This is the root command for actions that act on projects pipeline

Usage:
  icav2 projectpipelines [command]

Available Commands:
  create      Create a pipeline
  input       Retrieve input parameters of pipeline
  link        Link pipeline to a project
  list        List of pipelines for a project 
  start       Start a pipeline
  unlink      Unlink pipeline from a project

Flags:
  -h, --help   help for projectpipelines

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectpipelines [command] --help" for more information about a command.

icav2 projectpipelines create

This command creates a  pipeline in the current project

Usage:
  icav2 projectpipelines create [command]

Available Commands:
  cwl          Create a cwl pipeline
  cwljson      Create a cwl Json pipeline
  nextflow     Create a nextflow pipeline
  nextflowjson Create a nextflow Json pipeline

Flags:
  -h, --help                help for create
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectpipelines create [command] --help" for more information about a command.

icav2 projectpipelines create cwl

This command creates a CWL pipeline in the current project using the argument as code for the pipeline

Usage:
  icav2 projectpipelines create cwl [code] [flags]

Flags:
      --category stringArray   Category of the cwl pipeline. Add flag multiple times for multiple values.
      --comment string         Version comments
      --description string     (*) Description of pipeline
  -h, --help                   help for cwl
      --html-doc string        Html documentation for the cwl pipeline
      --links string           links in json format
      --parameter string       (*) Path to the parameter XML file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --project-id string      project ID to set current project context
      --proprietary            Add the flag if this pipeline is proprietary
      --storage-size string    (*) Name of the storage size. Can be fetched using the command 'icav2 analysisstorages list'.
      --tool stringArray       Path to the tool cwl file. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --workflow string        (*) Path to the workflow cwl file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines create cwljson

This command creates a CWL Json pipeline in the current project using the argument as code for the pipeline

Usage:
  icav2 projectpipelines create cwljson [code] [flags]

Flags:
      --category stringArray         Category of the cwl pipeline. Add flag multiple times for multiple values.
      --comment string               Version comments
      --description string           (*) Description of pipeline
  -h, --help                         help for cwljson
      --html-doc string              Html documentation for the cwl pipeline
      --inputForm string             (*) Path to the input form file.
      --links string                 links in json format
      --onRender string              Path to the on render file.
      --onSubmit string              Path to the on submit file.
      --otherInputForm stringArray   Path to the other input form files. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --project-id string            project ID to set current project context
      --proprietary                  Add the flag if this pipeline is proprietary
      --storage-size string          (*) Name of the storage size. Can be fetched using the command 'icav2 analysisstorages list'.
      --tool stringArray             Path to the tool cwl file. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --workflow string              (*) Path to the workflow cwl file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines create nextflow

This command creates a Nextflow pipeline in the current project

Usage:
  icav2 projectpipelines create nextflow [code] [flags]

Flags:
      --category stringArray      Category of the nextflow pipeline. Add flag multiple times for multiple values.
      --comment string            Version comments
      --config string             Path to the config nextflow file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --description string        (*) Description of pipeline
  -h, --help                      help for nextflow
      --html-doc string           Html documentation fo the nexflow pipeline
      --links string              links in json format
      --main string               (*) Path to the main nextflow file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --nextflow-version string   Version of nextflow language to use.
      --other stringArray         Path to the other nextflow file. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --parameter string          (*) Path to the parameter XML file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --project-id string         project ID to set current project context
      --proprietary               Add the flag if this pipeline is proprietary
      --storage-size string       (*) Name of the storage size. Can be fetched using the command 'icav2 analysisstorages list'.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines create nextflowjson

This command creates a Nextflow Json pipeline in the current project

Usage:
  icav2 projectpipelines create nextflowjson [code] [flags]

Flags:
      --category stringArray         Category of the nextflow pipeline. Add flag multiple times for multiple values.
      --comment string               Version comments
      --config string                Path to the config nextflow file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --description string           (*) Description of pipeline
  -h, --help                         help for nextflowjson
      --html-doc string              Html documentation fo the nexflow pipeline
      --inputForm string             (*) Path to the input form file.
      --links string                 links in json format
      --main string                  (*) Path to the main nextflow file. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --nextflow-version string      Version of nextflow language to use.
      --onRender string              Path to the on render file.
      --onSubmit string              Path to the on submit file.
      --other stringArray            Path to the other nextflow file. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --otherInputForm stringArray   Path to the other input form files. Add flag multiple times for multiple values. You can set a custom file name and path by adding ':filename=' and the filename with optionally the path the file should be located in.
      --project-id string            project ID to set current project context
      --proprietary                  Add the flag if this pipeline is proprietary
      --storage-size string          (*) Name of the storage size. Can be fetched using the command 'icav2 analysisstorages list'.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines input

Retrieve input parameters of pipeline

Usage:
  icav2 projectpipelines input [pipelineId] [flags]

Flags:
  -h, --help                help for input
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines link

This links a pipeline to a project. Use code or id to identifiy the pipeline. If code is not found, argument is used as id.

Usage:
  icav2 projectpipelines link [pipeline code] or [pipeline id] [flags]

Flags:
  -h, --help                       help for link
      --project-id string          project ID to set current project context
      --source-project-id string   project ID from where the pipeline needs to be linked, mandatory when using pipeline code

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines list

This command lists the pipelines for a given project

Usage:
  icav2 projectpipelines list [flags]

Flags:
  -h, --help                help for list
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines start

This command starts a  pipeline in the current project

Usage:
  icav2 projectpipelines start [command]

Available Commands:
  cwl          Start a CWL pipeline
  cwljson      Start a CWL Json pipeline
  nextflow     Start a Nextflow pipeline
  nextflowjson Start a Nextflow Json pipeline

Flags:
  -h, --help                help for start
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectpipelines start [command] --help" for more information about a command.

icav2 projectpipelines start cwl

This command starts a CWL pipeline for a given pipeline id, or for a pipeline code from the current project.

Usage:
  icav2 projectpipelines start cwl [pipeline id] or [code] [flags]

Flags:
      --data-id stringArray           Enter data id's as follows : dataId{optional-mount-path} . Add flag multiple times for multiple values.  Mount path is optional and can be absolute and relative and can not contain curly braces.
      --data-parameters stringArray   Enter data-parameters as follows : parameterCode:referenceDataId . Add flag multiple times for multiple values.
  -h, --help                          help for cwl
      --idempotency-key string        Add a maximum 255 character idempotency key to prevent duplicate requests. The  response is retained for 7 days so the key must be unique during that timeframe.
      --input stringArray             Enter inputs as follows : parametercode:dataId,dataId{optional-mount-path},dataId,... . Add flag multiple times for multiple values. Mount path is optional and can be absolute and relative and can not contain curly braces and commas.
      --input-json string             Analysis input JSON string. JSON input works only with file-based CWL pipelines (built using code, not a graphical editor in ICA).
      --output-parent-folder string   The id of the folder in which the output folder should be created.
      --parameters stringArray        Enter single-value parameters as code:value. Enter multi-value parameters as code:"'value1','value2','value3'". To add multiple values, add the flag multiple times.
      --project-id string             project ID to set current project context
      --reference-tag stringArray     Reference tag. Add flag multiple times for multiple values.
      --storage-size string           (*) Name of the storage size. Can be fetched using the command 'icav2 analysisstorages list'
      --technical-tag stringArray     Technical tag. Add flag multiple times for multiple values.
      --type-input string             (*) Input type STRUCTURED or JSON
      --user-reference string         (*) User reference
      --user-tag stringArray          User tag. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines start cwljson

This command starts a CWL Json pipeline for a given pipeline id, or for a pipeline code from the current project. See ICA CLI documentation for more information (https://help.ica.illumina.com/).

Usage:
  icav2 projectpipelines start cwljson [pipeline id] or [code] [flags]

Flags:
      --field stringArray             Fields. Add flag multiple times for multiple fields. --field fieldA:value --field multivalueFieldB:value1,value2
      --field-data stringArray        Data fields. Add flag multiple times for multiple fields. --field-data fieldA:fil.id --field-data multivalueFieldB:fil.id1,fil.id2
      --group stringArray             Groups. Add flag multiple times for multiple fields in the group. --group groupA.index1.multivalueFieldA:value1,value2 --group groupA.index1.fieldB:value --group groupB.index1.fieldA:value --group groupB.index2.fieldA:value
      --group-data stringArray        Data groups. Add flag multiple times for multiple fields in the group. --group-data groupA.index1.multivalueFieldA:fil.id1,fil.id2 --group-data groupA.index1.fieldB:fil.id --group-data groupB.index1.fieldA:fil.id --group-data groupB.index2.fieldA:fil.id
  -h, --help                          help for cwljson
      --idempotency-key string        Add a maximum 255 character idempotency key to prevent duplicate requests. The  response is retained for 7 days so the key must be unique during that timeframe.
      --output-parent-folder string   The id of the folder in which the output folder should be created.
      --project-id string             project ID to set current project context
      --reference-tag stringArray     Reference tag. Add flag multiple times for multiple values.
      --storage-size string           (*) Name of the storage size. Can be fetched using the command 'icav2  list'.
      --technical-tag stringArray     Technical tag. Add flag multiple times for multiple values.
      --user-reference string         (*) User reference
      --user-tag stringArray          User tag. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Field definition

A field can only have values (--field) and a data field can only have datavalues (--field-data). To create multiple fields or data fields, you have to repeat the flag.

For example

--field fieldA:valueA --fieldB multivalueFieldB:valueB1,valueB2 --field-data DataFieldC:file.id"

matches

    "fields": [
      {
        "id": "fieldA",
        "values": [
          "valueA"
        ]
      },
      {
        "id": "multivalueFieldB",
        "values": [
          "valueB1",
          "valueB2"
        ]
      },
      {
        "id": "DataFieldC",
        "values": [
          "file.id"
        ]
      }
    ]

The following example with --field and --field-data

--field asection:SECTION1
--field atext:"this is atext text"
--field ttt:tb1
--field notallowedrole:f
--field notallowedcondition:"this is a not allowed text box"
--field maxagesum:20
--field-data txts1:fil.ade9bd0b6113431a2de108d9fe48a3d8
--field-data txts2:fil.ade9bd0b6113431a2de108d9fe48a3d7{/dir1/dir2},fil.ade9bd0b6113431a2de108d9fe48a3d6{/dir3/dir4}

matches

    "fields": [
    {
      "id": "asection",
      "values": [
        "SECTION1"
      ]
    },
    {
      "id": "atext",
      "values": [
        "this is atext text"
      ]
    },
    {
      "id": "ttt",
      "values": [
        "tb1"
      ]
    },
    {
      "id": "notallowedrole",
      "values": [
        "f"
      ]
    },
    {
      "id": "notallowedcondition",
      "values": [
        "this is a not allowed text box"
      ]
    },
    {
      "id": "maxagesum",
      "values": [
        "20"
      ]
    },
    {
      "dataValues": [
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d8"
        }
      ],
      "id": "txts1"
    },
    {
      "dataValues": [
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d7",
          "mountPath": "/dir1/dir2"
        },
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d6",
          "mountPath": "/dir3/dir4"
        }
      ],
      "id": "txts2"
    }
  ],

Group definition

A group will only have values (--group) and a data group can only have datavalues (--group-data). Add flags multiple times for multiple groups and fields in the group.

--group group1.0.age:80
--group group1.0.role:f
--group group1.0.conditions:cancer,covid
--group-data group1.0.info:fil.a4f17ecf13ca4f692fd008d9fe48a3d7

--group group1.1.age:20
--group group1.1.role:m
--group-data group1.1.info:fil.a4f17ecf13ca4f692fd008d9fe48a3d7

--group group2.0.roleForGroup2:f

"groups": [
    {
      "id": "group1",
      "values": [
        {
          "values": [
            {
              "id": "age",
              "values": [
                "80"
              ]
            },
            {
              "id": "role",
              "values": [
                "f"
              ]
            },
            {
              "id": "conditions",
              "values": [
                "cancer",
                "covid"
              ]
            },
            {
              "dataValues": [
                {
                  "dataId": "fil.a4f17ecf13ca4f692fd008d9fe48a3d7"
                }
              ],
              "id": "info"
            }
          ]
        },
        {
          "values": [
            {
              "id": "age",
              "values": [
                "20"
              ]
            },
            {
              "id": "role",
              "values": [
                "m"
              ]
            },
            {
              "dataValues": [
                {
                  "dataId": "fil.a4f17ecf13ca4f692fd008d9fe48a3d7"
                }
              ],
              "id": "info"
            }
          ]
        }
      ]
    },
    {
      "id": "group2",
      "values": [
        {
          "values": [
            {
              "id": "roleForGroup2",
              "values": [
                "f"
              ]
            }
          ]
        }
      ]
    }
  ]

icav2 projectpipelines start nextflow

This command starts a Nextflow pipeline for a given pipeline id, or for a pipeline code from the current project.

Usage:
  icav2 projectpipelines start nextflow [pipeline id] or [code] [flags]

Flags:
      --data-parameters stringArray   Enter data-parameters as follows : parameterCode:referenceDataId . Add flag multiple times for multiple values.
  -h, --help                          help for nextflow
      --idempotency-key string        Add a maximum 255 character idempotency key to prevent duplicate requests. The  response is retained for 7 days so the key must be unique during that timeframe.
      --input stringArray             Enter inputs as follows : parametercode:dataId,dataId{optional-mount-path},dataId,... . Add flag multiple times for multiple values. Mount path is optional and can be absolute and relative and can not contain curly braces and commas.
      --output-parent-folder string   The id of the folder in which the output folder should be created.
      --parameters stringArray        Enter single-value parameters as code:value. Enter multi-value parameters as code:"'value1','value2','value3'". To add multiple values, add the flag multiple times.
      --project-id string             project ID to set current project context
      --reference-tag stringArray     Reference tag. Add flag multiple times for multiple values.
      --storage-size string           (*) Name of the storage size. Can be fetched using the command 'icav2  list'.
      --technical-tag stringArray     Technical tag. Add flag multiple times for multiple values.
      --user-reference string         (*) User reference
      --user-tag stringArray          User tag. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectpipelines start nextflowjson

This command starts a Nextflow Json pipeline for a given pipeline id, or for a pipeline code from the current project.  See ICA CLI documentation for more information (https://help.ica.illumina.com/).

Usage:
  icav2 projectpipelines start nextflowjson [pipeline id] or [code] [flags]

Flags:
      --field stringArray             Fields. Add flag multiple times for multiple fields. --field fieldA:value --field multivalueFieldB:value1,value2
      --field-data stringArray        Data fields. Add flag multiple times for multiple fields. --field-data fieldA:fil.id --field-data multivalueFieldB:fil.id1,fil.id2
      --group stringArray             Groups. Add flag multiple times for multiple fields in the group. --group groupA.index1.multivalueFieldA:value1,value2 --group groupA.index1.fieldB:value --group groupB.index1.fieldA:value --group groupB.index2.fieldA:value
      --group-data stringArray        Data groups. Add flag multiple times for multiple fields in the group. --group-data groupA.index1.multivalueFieldA:fil.id1,fil.id2 --group-data groupA.index1.fieldB:fil.id --group-data groupB.index1.fieldA:fil.id --group-data groupB.index2.fieldA:fil.id
  -h, --help                          help for nextflowjson
      --idempotency-key string        Add a maximum 255 character idempotency key to prevent duplicate requests. The  response is retained for 7 days so the key must be unique during that timeframe.
      --output-parent-folder string   The id of the folder in which the output folder should be created.
      --project-id string             project ID to set current project context
      --reference-tag stringArray     Reference tag. Add flag multiple times for multiple values.
      --storage-size string           (*) Name of the storage size. Can be fetched using the command 'icav2  list'.
      --technical-tag stringArray     Technical tag. Add flag multiple times for multiple values.
      --user-reference string         (*) User reference
      --user-tag stringArray          User tag. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Field definition

A field can only have values (--field) and a data field can only have datavalues (--field-data). To create multiple fields or data fields, you have to repeat the flag.

For example

--field fieldA:valueA --fieldB multivalueFieldB:valueB1,valueB2 --field-data DataFieldC:file.id"

matches

    "fields": [
      {
        "id": "fieldA",
        "values": [
          "valueA"
        ]
      },
      {
        "id": "multivalueFieldB",
        "values": [
          "valueB1",
          "valueB2"
        ]
      },
      {
        "id": "DataFieldC",
        "values": [
          "file.id"
        ]
      }
    ]

The following example with --field and --field-data

--field asection:SECTION1
--field atext:"this is atext text"
--field ttt:tb1
--field notallowedrole:f
--field notallowedcondition:"this is a not allowed text box"
--field maxagesum:20
--field-data txts1:fil.ade9bd0b6113431a2de108d9fe48a3d8
--field-data txts2:fil.ade9bd0b6113431a2de108d9fe48a3d7{/dir1/dir2},fil.ade9bd0b6113431a2de108d9fe48a3d6{/dir3/dir4}

matches

    "fields": [
    {
      "id": "asection",
      "values": [
        "SECTION1"
      ]
    },
    {
      "id": "atext",
      "values": [
        "this is atext text"
      ]
    },
    {
      "id": "ttt",
      "values": [
        "tb1"
      ]
    },
    {
      "id": "notallowedrole",
      "values": [
        "f"
      ]
    },
    {
      "id": "notallowedcondition",
      "values": [
        "this is a not allowed text box"
      ]
    },
    {
      "id": "maxagesum",
      "values": [
        "20"
      ]
    },
    {
      "dataValues": [
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d8"
        }
      ],
      "id": "txts1"
    },
    {
      "dataValues": [
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d7",
          "mountPath": "/dir1/dir2"
        },
        {
          "dataId": "fil.ade9bd0b6113431a2de108d9fe48a3d6",
          "mountPath": "/dir3/dir4"
        }
      ],
      "id": "txts2"
    }
  ],

Group definition

A group will only have values (--group) and a data group can only have datavalues (--group-data). Add flags multiple times for multiple groups and fields in the group.

--group group1.0.age:80
--group group1.0.role:f
--group group1.0.conditions:cancer,covid
--group-data group1.0.info:fil.a4f17ecf13ca4f692fd008d9fe48a3d7

--group group1.1.age:20
--group group1.1.role:m
--group-data group1.1.info:fil.a4f17ecf13ca4f692fd008d9fe48a3d7

--group group2.0.roleForGroup2:f

"groups": [
    {
      "id": "group1",
      "values": [
        {
          "values": [
            {
              "id": "age",
              "values": [
                "80"
              ]
            },
            {
              "id": "role",
              "values": [
                "f"
              ]
            },
            {
              "id": "conditions",
              "values": [
                "cancer",
                "covid"
              ]
            },
            {
              "dataValues": [
                {
                  "dataId": "fil.a4f17ecf13ca4f692fd008d9fe48a3d7"
                }
              ],
              "id": "info"
            }
          ]
        },
        {
          "values": [
            {
              "id": "age",
              "values": [
                "20"
              ]
            },
            {
              "id": "role",
              "values": [
                "m"
              ]
            },
            {
              "dataValues": [
                {
                  "dataId": "fil.a4f17ecf13ca4f692fd008d9fe48a3d7"
                }
              ],
              "id": "info"
            }
          ]
        }
      ]
    },
    {
      "id": "group2",
      "values": [
        {
          "values": [
            {
              "id": "roleForGroup2",
              "values": [
                "f"
              ]
            }
          ]
        }
      ]
    }
  ]

icav2 projectpipelines unlink

This unlinks a pipeline from a project. Use code or id to identifiy the pipeline. If code is not found, argument is used as id.

Usage:
  icav2 projectpipelines unlink [pipeline code] or [pipeline id] [flags]

Flags:
  -h, --help                help for unlink
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projects

This is the root command for actions that act on projects

Usage:
  icav2 projects [command]

Available Commands:
  create      Create a project
  enter       Enter project context
  exit        Exit project context
  get         Get details of a project
  list        List projects

Flags:
  -h, --help   help for projects

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projects [command] --help" for more information about a command.

icav2 projects create

This command creates a project.

Usage:
  icav2 projects create [projectname] [flags]

Flags:
      --billing-mode string                Billing mode , defaults to PROJECT (default "PROJECT")
      --data-sharing                       Indicates whether the data and samples created in this project can be linked to other Projects. This flag needs no value, adding it sets the value to true.
  -h, --help                               help for create
      --info string                        Info about the project
      --metadata-model string              Id of the metadata model. 
      --owner string                       Owner of the project. Default is the current user
      --region string                      Region of the project. When not specified : takes a default when there is only 1 region, else a choice will be given.
      --short-descr string                 Short pipelineDescription of the project
      --storage-bundle string              Id of the storage bundle. When not specified : takes a default when there is only 1 bundle, else a choice will be given. 
      --storage-config string              An optional storage configuration id to have self managed storage.
      --storage-config-sub-folder string   Required when specifying a storageConfigurationId. The subfolder determines the object prefix of your self managed storage.
      --technical-tag stringArray          Technical tags for this project. Add flag multiple times for multiple values.
      --user-tag stringArray               User tags for this project. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projects enter

This command sets the project context for future commands

Usage:
  icav2 projects enter [projectname] or [project id] [flags]

Flags:
  -h, --help   help for enter

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projects exit

This command switches the user back to their personal context

Usage:
  icav2 projects exit [flags]

Flags:
  -h, --help                help for exit
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projects get

This command fetches the details of the current project. If no project id is given, we take the one from the config file.

Usage:
  icav2 projects get [project id] [flags]

Flags:
  -h, --help   help for get

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projects list

This command lists the projects for the current user. Page-offset can only be used in combination with sort-by. Sorting can be done on 
- name
- shortDescription
- information

Usage:
  icav2 projects list [flags]

Flags:
  -h, --help              help for list
      --max-items int     maximum number of items to return, the limit and default is 1000
      --page-offset int   Page offset, only used in combination with sort-by. Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages
      --page-size int32   Page size, only used in combination with sort-by. The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --sort-by string    specifies the order to list items

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples

This is the root command for actions that act on projects samples

Usage:
  icav2 projectsamples [command]

Available Commands:
  complete    Set sample to complete
  create      Create a sample for a project
  delete      Delete a sample for a project
  get         Get details of a sample
  link        Link data to a sample for a project
  list        List of samples for a project 
  listdata    List data from given sample
  unlink      Unlink data from a sample for a project
  update      Update a sample for a project

Flags:
  -h, --help   help for projectsamples

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectsamples [command] --help" for more information about a command.

icav2 projectsamples complete

The sample status will be set to 'Available' and a sample completed event will be triggered as well.

Usage:
  icav2 projectsamples complete [sampleId] [flags]

Flags:
  -h, --help                help for complete
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples create

This command creates a sample for a project. It takes the name of the sample as argument.

Usage:
  icav2 projectsamples create [name] [flags]

Flags:
      --description string          Description 
  -h, --help                        help for create
      --project-id string           project ID to set current project context
      --technical-tag stringArray   Technical tag. Add flag multiple times for multiple values.
      --user-tag stringArray        User tag. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples delete

This command deletes a sample from a project. The different flags indicate the way they are deleted. Only 1 flag can be used.

Usage:
  icav2 projectsamples delete [sampleId] [flags]

Flags:
      --deep         Delete the entire sample: sample and linked files will be deleted from your project.
  -h, --help         help for delete
      --mark         Mark a sample as deleted.
      --unlink       Unlinking the sample: sample is deleted and files are unlinked and available again for linking to another sample.
      --with-input   Delete the sample as well as its input data: sample is deleted from your project, the input files and pipeline output folders are still present in the project but will not be available for linking to a new sample.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples get

This command fetches the details a sample using the argument as a name, if nothing found, the argument is used as an id (uuid).

Usage:
  icav2 projectsamples get [sample id] or [name] [flags]

Flags:
  -h, --help                help for get
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples link

This command adds data to a project sample. Argument is the id of the project sample

Usage:
  icav2 projectsamples link [sampleId] [flags]

Flags:
      --data-id stringArray   (*) Data id of the data that needs to be linked to the project sample. Add flag multiple times for multiple values.
  -h, --help                  help for link
      --project-id string     project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples list

This command lists the samples for a given project

Usage:
  icav2 projectsamples list [flags]

Flags:
  -h, --help                        help for list
      --include-deleted             Include the deleted samples in the list. Default set to false.
      --project-id string           project ID to set current project context
      --technical-tag stringArray   Technical tags to filter on. Add flag multiple times for multiple values.
      --user-tag stringArray        User tags to filter on. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples listdata

This command lists the data for a given sample. It only supports offset based, and default sorting is done on timeCreated. Sorting can be done on timeCreated
- timeModified
- name
- path
- fileSizeInBytes
- status
- format
- dataType
- willBeArchivedAt
- willBeDeletedAt

Usage:
  icav2 projectsamples listdata [sampleId] [path] [flags]

Flags:
      --data-type string        Data type. Available values : FILE or FOLDER
      --file-name stringArray   The filenames to filter on. The filenameMatchMode-parameter determines how the filtering is done. Add flag multiple times for multiple values.
  -h, --help                    help for listdata
      --match-mode string       Match mode for the file name. Available values : EXACT (default), EXCLUDE, FUZZY.
      --max-items int           maximum number of items to return, the limit and default is 1000
      --page-offset int         Page offset, only used in combination with sort-by. Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages
      --page-size int32         Page size, only used in combination with sort-by. The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --parent-folder           Indicates that the given argument is path of the parent folder. All children are selected for list, not the folder itself. This flag needs no value, adding it sets the value to true.
      --project-id string       project ID to set current project context
      --sort-by string          specifies the order to list items (default "timeCreated Desc")
      --status stringArray      Add the status of the data. Available values : PARTIAL, AVAILABLE, ARCHIVING, ARCHIVED, UNARCHIVING, DELETING. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples unlink

This command removes data from a project sample. Argument is the id of the project sample

Usage:
  icav2 projectsamples unlink [sampleId] [flags]

Flags:
      --data-id stringArray   (*) Data id of the data that will be removed from the project sample. Add flag multiple times for multiple values.
  -h, --help                  help for unlink
      --project-id string     project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectsamples update

This command updates a sample for a project. Name,description, user and technical tags can be updated

Usage:
  icav2 projectsamples update [sampleId] [flags]

Flags:
      --add-tech-tag stringArray      Tech tag to add. Add flag multiple times for multiple values.
      --add-user-tag stringArray      User tag to add. Add flag multiple times for multiple values.
  -h, --help                          help for update
      --name string                   Name 
      --project-id string             project ID to set current project context
      --remove-tech-tag stringArray   Tech tag to remove. Add flag multiple times for multiple values.
      --remove-user-tag stringArray   User tag to remove. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 regions

This is the root command for actions that act on regions

Usage:
  icav2 regions [command]

Available Commands:
  list        list of regions

Flags:
  -h, --help   help for regions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 regions [command] --help" for more information about a command.

icav2 regions list

This command lists all the regions

Usage:
  icav2 regions list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 storagebundles

This is the root command for actions that act on storage bundles

Usage:
  icav2 storagebundles [command]

Available Commands:
  list        list of storage bundles

Flags:
  -h, --help   help for storagebundles

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 storagebundles [command] --help" for more information about a command.

icav2 storagebundles list

This command lists all the storage bundles id's

Usage:
  icav2 storagebundles list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 storageconfigurations

This is the root command for actions that act on storage configurations

Usage:
  icav2 storageconfigurations [command]

Available Commands:
  list        list of storage configurations

Flags:
  -h, --help   help for storageconfigurations

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 storageconfigurations [command] --help" for more information about a command.

icav2 storageconfigurations list

This command lists all the storage configurations

Usage:
  icav2 storageconfigurations list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 tokens

This is the root command for actions that act on tokens

Usage:
  icav2 tokens [command]

Available Commands:
  create      Create a JWT token
  refresh     Refresh a JWT token from basic authentication

Flags:
  -h, --help   help for tokens

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 tokens [command] --help" for more information about a command.

icav2 tokens create

This command creates a JWT token from the API key.

Usage:
  icav2 tokens create [flags]

Flags:
  -h, --help   help for create

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 tokens refresh

This command refreshes a JWT token from basic authentication with gantype JWT-bearer that is set with the -t flag.

Usage:
  icav2 tokens refresh [flags]

Flags:
  -h, --help   help for refresh

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 version

The version of this application

Usage:
  icav2 version [flags]

Flags:
  -h, --help   help for version

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service