create

create

The create command can be used to easily generate CWL CommandLineTools. It serves as a prefix to the usual command line prompt. Calling create with a command attached will execute the command, determine in- and outputs and create a CWL tool definition file in the workflows folder.

Note

Before using this command all changes need to be commited as it uses git to determine tool outputs! git status can be used to check beforehand.

Tip

Redirection > and pipes | can be used, but need to be escaped with a backslash fot the parser to use. Otherwise the console output of s4n will be redirected / piped.

Usage

    Creates a new CWL File or Workflow

    Usage: s4n create [OPTIONS] [COMMAND]...

    Arguments:
      [COMMAND]...  Command line call e.g. python script.py [ARGUMENTS]

    Options:
      -n, --name <NAME>                        A name to be used for this workflow or tool
      -c, --container-image <CONTAINER_IMAGE>  An image to pull from e.g. docker hub or path to a Dockerfile
      -t, --container-tag <CONTAINER_TAG>      The tag for the container when using a Dockerfile
      -r, --raw                                Outputs the raw CWL contents to terminal
          --no-commit                          Do not commit at the end of tool creation
          --no-run                             Do not run given command
          --clean                              Deletes created outputs after usage
          --no-defaults                        Removes default values from inputs
          --net                                Enables network in container
      -i, --inputs <INPUTS>                    Force values to be considered as an input.
      -o, --outputs <OUTPUTS>                  Force values to be considered as an output.
      -m, --mount <MOUNT>                      Mounts a directory into the working directory
      -f, --force                              Overwrites existing workflow
      -h, --help                               Print help

Example

The following command will create a CWL CommandLineTool description for executing a python script echo.py with a txt file as parameter --test.

s4n create python echo.py --test input.txt

The command will create this CWL file in the workflows folder.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

requirements:
- class: InitialWorkDirRequirement
  listing:
  - entryname: echo.py
    entry:
      $include: '../../echo.py'

inputs:
- id: test
  type: File
  default:
    class: File
    location: '../../input.txt'
  inputBinding:
    prefix: '--test'

outputs:
- id: results
  type: File
  outputBinding:
    glob: results.txt

baseCommand:
- python
- echo.py

Options

If only --name is given the command will create an empty workflow. However this is completely optional as the workflow will also be created upon the creating the first connection.

With the --name option the resulting filename can be manipulated. Without the argument SciWIn client will automatically generate a name based on the command. If for example the same base command is used in two tools there would be a file name conflict.

The two container options --container-image and --container-tag can be used to add Docker requirements to the resulting CWL file. However Docker will NOT be used to execute the script while generating the tool, so make sure to either use s4n in Docker container or provide all neccesary tools for it to run.

With the --raw flag no CWL file will be written to disk. Instead the raw cwl will be outputted to the command prompt (stdout) to process it further.

As create needs all changes to be commited beforehand it will create a commit after it completed the tool creation. To prevent that because e.g. manual changes to the CWL file have to be made before committing the --no-commit flag can be used.

Some scripts tend to run for a very long time - e.g. quantum chemistry calculations. To prevent the tool from running the --no-run flag can be used. If this flag is set the parser will just use information from the command line to create the tool, outputs need to be set manually.

Sometimes it can be beneficial to not commit the created outputs. With the --clean flag all outputs will be deleted before commiting the freshly created tool.

Implicit in- and outputs can be added using -i or -o. (See Examples)