Staging Folders

CWL stages all input files and directories in a random read-only temp directory away from the working directory. If these are part of the basecommand, arguments, or have an inputBinding, CWL will handle the file paths for you. However you the above limitations will not work in the following situations:

  1. The File or Directory needs to be staged in the Docker image, but is not part of the command.
  2. You need to change the file or directory in some way.
  3. You need the file or directory to be in the working directory.
  4. The path to the file or directory needs to be predictable.

Part 1: Input files in the working directory

Here is a python script that can use the sync to synapse function:

import synapseclient
import argparse
import synapseutils

if __name__ == '__main__':

    parser = argparse.ArgumentParser("Stores files in Synapse")

            type = str,

            type = str,

    args = parser.parse_args()

    syn = synapseclient.Synapse(configPath=args.synapse_config_file)

    synapseutils.sync.syncToSynapse(syn, args.manifest_file)

And here is the CWL tool that calls it:

#!/usr/bin/env cwl-runner
# Authors: Andrew Lamb

cwlVersion: v1.0
class: CommandLineTool

- class: InitialWorkDirRequirement
  listing: $(inputs.files)


- python3
- /usr/local/bin/


  files: File[]

    type: File
      prefix: "--synapse_config_file"

    type: File
      prefix: "--manifest_file"

outputs: []

In the above example we need to pass a manifest to the tool that has the paths of the files to be uploaded. If we didn’t stage the files in the working directory, CWL would put them all in their own randomly generated temp directories. By placing them in the working directory we know that the relative paths will be just the name of the file.

To stage the files specified in the input files parameter we include the following:

- class: InitialWorkDirRequirement
  listing: $(inputs.files)

Notice that the below input does not have an inputBinding. This means its a parameter of the tool, but not the command the tool is constructing. This allows the file parameter to be referenced by the InitialWorkDirRequirement:

Part 2: Creating a config file in the working directory

The below tool needs a config file, where the last line is a directory that is being passed in an input. The directory will be put in a random location in the docker image, so the config file cannot be passed in as an input as well, but needs to be written after the path to the directory is known.

baseCommand: run-pipe

- --config
- config_drops.ini

  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
      - entryname: config_drops.ini
        entry: |
          samtools = samtools
          star = STAR
          whitelistDir = /usr/app/baseqDrops/whitelist
          cellranger_ref_hg38 = $(inputs.index_dir.path)

- id: index_dir
  type: Directory

The above tool produces a file called config_drops.ini in the working directory with 4 lines. The first three refer to paths in the docker image, the fourth line refers the input directory and will put the path generated by CWL into the config file.

Part 3: Making an input file or directory writable

If you need to make a file writable you can use the writable attribute:

  - class: InitialWorkDirRequirement
      - entry: $(inputs.input_file)
         writable: true

- id: input_file
  type: File