Mounting specific output directory

CWL Questions
1

Hello all! Currently, I am running docker images like so. This image below simply does an “ls /input > /output/predictions.csv”

mkdir folder
touch folder/fee
mkdir test
docker run -v $(pwd)/folder:/input:ro -v $(pwd)/test:/output:rw thomasvyu/challenge-example:latest
ls test/
predictions.csv

We specify a specific directory to write to in the container like /output. Is it possible to mimic this behavior with CWL:

cwlVersion: v1.0
class: CommandLineTool

requirements:
  - class: DockerRequirement
    dockerPull: ...
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entry: $(inputs.input)
        entryname: $("/input") 
      - entry: $(inputs.output)
        entryname: $("/output") 
        writable: true


inputs:
  - id: input
    type: Directory
  - id: output
    type: Directory

outputs:
  - id: prediction_file
    type: File
    outputBinding:
      glob: $(inputs.output.path + "/prediction.csv")

I tried the above, but that doesn’t work.

2

Hi @thomasyu888, could you post a sample error log please. Two things to try

  1. Don’t have the entryname be a parameter reference (not needed).
  2. Use a relative path, rather than an absolute path
  - class: InitialWorkDirRequirement
    listing:
      - entry: $(inputs.input)
        entryname: input 
      - entry: $(inputs.output)
        entryname: output 
        writable: true
3

HI @kaushik-work,

Thanks for the prompt response. I found what I was looking for:

#!/usr/bin/env cwl-runner
#
# Run a docker image
#
cwlVersion: v1.0
class: CommandLineTool

requirements:
  - class: DockerRequirement
    dockerPull: thomasvyu/challenge-example:latest
    dockerOutputDirectory: /output
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entry: $(inputs.input)
        entryname: $("/input") 

inputs:
  - id: input
    type: Directory

outputs:
  - id: pred
    type: File
    outputBinding:
      glob: $("predictions.csv")
4

Here’s a version that doesn’t required InlineJavascriptRequirement

#!/usr/bin/env cwl-runner
#
# Run a docker image
#
cwlVersion: v1.0
class: CommandLineTool

requirements:
  DockerRequirement:
    dockerPull: thomasvyu/challenge-example:latest
    dockerOutputDirectory: /output
 InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.input)
        entryname: input

inputs:
  input:
    type: Directory

outputs:
  pred:
    type: File
    outputBinding:
      glob: predictions.csv
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