$ formbio --help
manages Formbio workflows, storage and resources.

Usage:
  formbio [command]

Available Commands:
  auth        Runs authentication subcommands
  completion  Generate the autocompletion script for the specified shell
  help        Help about any command
  storage     Runs storage subcommands
  version     Version will output the current build information
  workflow    Runs workflow subcommands

Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.
  -h, --help            help for formbio

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

$ formbio auth --help
Runs authentication subcommands

Usage:
  formbio auth [command]

Available Commands:
  login       Authenticates with the Form Bio platform for running CLI commands
  logout      Logs the current user out
  whoami      Prints the current user's email

Flags:
  -h, --help   help for auth

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

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

$ formbio storage --help
Runs storage subcommands

Usage:
  formbio storage [command]

Available Commands:
  cp          Copies and object or tree of objects
  ls          Lists the stored objects for a specific project

Flags:
  -h, --help   help for storage

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

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

$ formbio workflow run --help
Runs a Nextflow workflow through the Form Bio platform

Usage:
  formbio workflow run --org org --project project --repo repo --version version --run-name runName  -- [--paramName <param-value>] [--paramName2 <param-value>] [flags]

Examples:
formbio workflow run --org=org-production --project=projectA --repo=formbio/nf-examplepipeline --version=main --run-name="testInputs" -- --input "formbio://org-slug/project-slug/sequencing" --batchFile "formbio://org-slug/project-slug/design.batch"

Flags:
      --config string                  If --workflow-container is true, a stringified JSON object containing container config values (e.g. '{"inputs": ["filePath1"], "outputs": ["outputs/"]}')
      --config-file string             If --workflow-container is true, the location of a .json file containing container-config options
  -h, --help                           help for run
      --nextflow-params string         Nextflow pipeline params JSON e.g. --nextflow-params='{"input": "gs://test-bucket/test.txt", "batchInput": "gs://test-bucket/test.batch"}'
      --nextflow-version string        The version of Nextflow that you want to use for your workflow run.
      --org string                     The slug of the organization you are accessing.
      --project string                 The slug of the project you are accessing.
      --repo string                    The repository you want to source for your Nextflow script (e.g. formbio/nf-proteingetinfo).
      --require-schema-validation      If set to true, a workflow run will not be started unless the inputs can be validated against the workflow schema. (default true)
      --run-name string                The name of the pipeline run that it will be indexed under.
      --set-default-inputs             If set to true, empty workflow inputs will be auto-filled with default values (if available). (default true)
      --skip-workflow-results string   Skip running workflow, copy provided workflow results to output folder. Must be in "org://project/workflow_run_id" format.
      --timeout duration               Timeout for running Nextflow on google life sciences. (default 720h0m0s)
      --version string                 Github branch or tag to run (e.g. main or v1.0.2).
      --workflow string                The name of the workflow you are running.
      --workflow-container             If set to true, workflow container will run directly rather than use an uploaded workflow. Must include --config or --config-file

Global Flags:
      --debug   Print debug log lines in the CLI console.

$ formbio auth login --help
Authenticates with the Form Bio platform for running CLI commands

Usage:
  formbio auth login [flags]

Flags:
  -h, --help   help for login

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

Authenticating Form Bio CLI...
Log in at https://form.bio/auth/login-token/, then copy/paste your Form Bio CLI API Token below...
Enter the CLI API Token:


// User's browser will open to the Form Bio platform where they can
// 1. Log in with email and password
// 2. Log in with Google Signin

// Once user pastes in the CLI API Token, they will see this message:
Authenticated as [user@email.com]
To switch users, use:
        formbio auth logout

Already authenticated as [user@email.com] - to switch users, use:
        formbio auth logout

$ formbio auth logout --help
Logs the current user out

Usage:
  formbio auth logout [flags]

Flags:
      --env string   The Bantha environment you want to access [local|dev|sbx|stg|prod].
  -h, --help         help for logout

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

You have successfully logged out.

$ formbio auth whoami --help
Prints the current user's email

Usage:
  formbio auth whoami [flags]

Aliases:
  whoami, who

Flags:
      --env string   The Bantha environment you want to access [local|dev|sbx|stg|prod].
  -h, --help         help for whoami

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

You are currently authenticated as Form Bio user user@email.com

$ formbio storage ls --help
Lists the stored objects for a specific organization and project. The path should be in the format "formbio://<organization>/<project>/<prefix>".

Usage:
  formbio storage ls [-r | --recursive] <path> [flags]

Examples:
  # list the root level objects for a project
  formbio storage ls --env=prod formbio://my-organization/my-project/

  # recursively list the objects in a specific directory
  formbio storage ls --env=prod -r formbio://my-organization/my-project/workflow-input-files/

Flags:
      --env string   The Bantha environment you want to access [local|dev|sbx|stg|prod].
  -h, --help         help for ls
  -r, --recursive    List objects recursively, default is non-recursive.

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

Authenticating on the "prod" environment
Authenticated as [my_user@formbio.com] on the prod environment
Looking up stored objects

total objects: 3

formbio://my-organization/my-project/:
            2022-06-23T23:54:20Z  formbio://my-organization/my-project/logs/
            2022-10-07T05:18:53Z  formbio://my-organization/my-project/my_file.txt

Authenticating on the "prod" environment
Authenticated as [my_user@formbio.com] on the prod environment
Looking up stored objects

total objects: 2

formbio://my-organization/my-project/logs/:
                                  formbio://my-organization/my-project/logs/end/

formbio://my-organization/my-project/logs/end/:
                                  formbio://my-organization/my-project/logs/end/of/

formbio://my-organization/my-project/logs/end/of/:
                                  formbio://my-organization/my-project/logs/end/of/the/

formbio://my-organization/my-project/logs/end/of/the/:
                                  formbio://my-organization/my-project/logs/end/of/the/rainbow/

formbio://my-organization/my-project/logs/end/of/the/rainbow/:
    338361  2022-10-07T05:21:09Z  formbio://my-organization/my-project/logs/end/of/the/rainbow/pot-of-gold.png

Copies and object or tree of objects from source to target, used for downloading, uploading, and copying, where source and target can be either local paths or formbio URLs in the format "formbio://<organization>/<project>/<prefix>".

Usage:
  formbio storage cp [-r | --recursive] [-c | --continue] <source> <target> [flags]

Examples:
  # upload single file to a directory
  formbio storage cp --env=prod myfile.txt formbio://my-organization/my-project/

  # download a directory into the current local directory
  formbio storage cp --env=prod -r formbio://my-organization/my-project/workflow-input-files/ .

  # copy a directory from one project into another
  formbio storage cp --env=prod -r formbio://my-organization/project-a/my-dataset/ formbio://my-organization/project-b/my-dataset/

Flags:
  -c, --continue     To resume an uploaded previously partially completed, use the continue flag.
      --env string   The Bantha environment you want to access [local|dev|sbx|stg|prod].
  -h, --help         help for cp
  -r, --recursive    To copy a tree of objects, specify a recursive copy.

Global Flags:
      --config string   Select your config file (default is $HOME/.formbio.yaml).
      --debug           Print debug log lines in the CLI console.

Authenticating on the "prod" environment
Authenticated as [user@formbio.com] on the prod environment
Starting download

Preparing Download   █████████████████████████████████████████████████ 100% | 0s
 SUCCESS  logs/my_file.txt                                                                                                                                                                                                  
DownloadingFiles     █████████████████████████████████████████████████ 100% | 0s

Files Downloaded:      1/1
Total Data Downloaded: 104 KiB/104 KiB
Download complete

Authenticating on the "prod" environment
Authenticated as [user@formbio.com] on the prod environment
Starting upload

Preparing Upload     █████████████████████████████████████████████████ 100% | 1s
 SUCCESS  formbio://my-organization/my-project/my_file.txt
Uploading Files      █████████████████████████████████████████████████ 100% | 1s

Files Uploaded:      1/1
Total Data Uploaded: 104 KiB/104 KiB
Upload complete

Authenticating on the "prod" environment
Authenticated as [user@formbio.com] on the prod environment
Starting upload

Preparing Upload     █████████████████████████████████████████████████ 100% | 2s
 SUCCESS  formbio://my-organization/my-project/logs/subdir/mylocaldir/my_file1.txt
 SUCCESS  formbio://my-organization/my-project/logs/subdir/mylocaldir/my_file2.txt
Uploading Files      █████████████████████████████████████████████████ 100% | 1s

Files Uploaded:      2/2
Total Data Uploaded: 209 KiB/209 KiB
Upload complete

Authenticating on the "prod" environment
Authenticated as [user@formbio.com] on the prod environment
Starting upload

Preparing Upload     █████████████████████████████████████████████████ 100% | 1s
Uploading Files      ███████████████████████████████████████            79% | 0s

Authenticating on the "prod" environment
Authenticated as [user@formbio.com] on the prod environment
Successfully created new directory

$ ./bin/formbio workflow run --help
Runs a Nextflow workflow through the Form Bio platform

Usage:
  formbio workflow run --org org --project project --repo repo --version version --run-name runName  -- [--paramName <param-value>] [--paramName2 <param-value>] [flags]

Examples:
formbio workflow run --org=org-production --project=projectA --repo=formbio/nf-examplepipeline --version=main --run-name="testInputs" -- --input "formbio://org-slug/project-slug/sequencing" --batchFile "formbio://org-slug/project-slug/design.batch"

Flags:
      --config string                  If --workflow-container is true, a stringified JSON object containing container config values (e.g. '{"inputs": ["filePath1"], "outputs": ["outputs/"]}')
      --config-file string             If --workflow-container is true, the location of a .json file containing container-config options
  -h, --help                           help for run
      --nextflow-params string         Nextflow pipeline params JSON e.g. --nextflow-params='{"input": "gs://test-bucket/test.txt", "batchInput": "gs://test-bucket/test.batch"}'
      --nextflow-version string        The version of Nextflow that you want to use for your workflow run.
      --org string                     The slug of the organization you are accessing.
      --project string                 The slug of the project you are accessing.
      --repo string                    The repository you want to source for your Nextflow script (e.g. formbio/nf-proteingetinfo).
      --require-schema-validation      If set to false, a workflow run will submit even if the inputs fail to validate against the workflow schema. (default true)
      --run-name string                The name of the pipeline run that it will be indexed under.
      --set-default-inputs             If set to false, empty workflow inputs will not be auto-filled with available default values. (default true)
      --skip-workflow-results string   Skip running workflow, copy provided workflow results to output folder. Must be in "org://project/workflow_run_id" format.
      --timeout duration               Timeout for running Nextflow on google life sciences. (default 720h0m0s)
      --version string                 Github branch or tag to run (e.g. main or v1.0.2).
      --workflow string                The name of the workflow you are running.
      --workflow-container             If set to true, workflow container will run directly rather than use an uploaded workflow. Must include --config or --config-file

Global Flags:
      --debug   Print debug log lines in the CLI console.