workflows versions files

Prints or downloads workflow files

Synopsis

omics workbench workflows versions files --workflow=WORKFLOW_ID [VERSION_ID]
  [--path=PATH]
  [--output=PATH]
  [--zip]

Description

Retrieve files belonging to a workflow version using the provided WORKFLOW_ID and VERSION_ID parameters. Behaviour depends on the values set for the flags. See the examples below for more information.

Examples

Prints out the workflow's descriptor file to the screen:

omics workbench workflows versions files --workflow=12345678910 1.0.0

Prints the workflow file matching the given path to the screen. If the file is binary, the file contents will not be printed to the screen and a warning will be printed instead:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --path=my/path/file.wdl

Saves the content from the --path file as a file in the location specified by --output:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --path=my/path/file.wdl
  --output=output/new_file.txt

Saves all the workflow's files in the same hierarchy in the location specified by --output. Note: --output must end with a folder in order to store all the workflow's files:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --output=output/folder

Downloads the file specified by --path as a zip file in the location specified by --output:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --path=my/path/file.wdl
  --output=output/new_file.zip
  --zip

Downloads the file specified by --path as a zip file named 12345678910-1.0.0-files.zip ({workflow_name}-{workflow_version}-files.zip) in the folder location specified by --output:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --path=my/path/file.wdl
  --output=output/folder
  --zip

Downloads the file specified by --path as a zip file named 12345678910-1.0.0-files.zip in the current working directory:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --path=my/path/file.wdl
  --zip

Downloads all files in the workflow in the zip file location specified by --output:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --output=output/all_files.zip
  --zip

Downloads all files in the workflow as a zip file named 12345678910-1.0.0-files.zipin the folder location specified by --output:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --output=output/all_files
  --zip

Downloads all files in the workflow as a zip file named 12345678910-1.0.0-files.zip in the current working directory:

omics workbench workflows versions files --workflow=12345678910 1.0.0 \
  --zip

Positional Arguments

VERSION_ID

Required. Specify a version identifier (VERSION_ID) to retrieve the files corresponding to the workflow's specific version.

Flags

--workflow=WORKFLOW_ID

Required. Specify the UUID of the workflow for which you want to describe versions.

--path=PATH

The path for the specific file in the workflow that is to be printed to the screen or downloaded.

--output=PATH

The location where a workflow file or files will be downloaded. Note: if --path is not specified (i.e. you are downloading multiple files) then --output must end with a folder and not an existing file name.

--zip

If specified, the file(s) will be downloaded as into a zip file. Note: if --output is not specified or does not end with a zip file, then it will create a zip file with the naming convention {workflow_name}-{workflow_version}-files.zip.