Staging Input Files

Overview

Teaching: 10 min
Exercises: 0 min
Questions
  • How do I stage input files in the working directory?

Objectives
  • Learn how to handle situations where a tool expects to write output files to the same directory as its input files.

Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use InitialWorkDirRequirement to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path.

linkfile.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
hints:
  DockerRequirement:
    dockerPull: openjdk:9.0.1-11-slim
baseCommand: javac

requirements:
  InitialWorkDirRequirement:
    listing:
      - $(inputs.src)

inputs:
  src:
    type: File
    inputBinding:
      position: 1
      valueFrom: $(self.basename)

outputs:
  classfile:
    type: File
    outputBinding:
      glob: "*.class"

arguments-job.yml

src:
  class: File
  path: Hello.java

Now invoke cwl-runner with the tool wrapper and the input object on the command line:

$ cwl-runner linkfile.cwl arguments-job.yml
[job 139928309171664] /home/example$ docker run -i --volume=/home/example/Hello.java:/var/lib/cwl/job557617295_examples/Hello.java:ro --volume=/home/example:/var/spool/cwl:rw --volume=/tmp/tmpmNbApw:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1001 --rm --env=TMPDIR=/tmp java:7 javac Hello.java
Final process status is success
{
"classfile": {
  "size": 416,
  "location": "/home/example/Hello.class",
  "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
  "class": "File"
  }
}

Key Points

  • Input files are normally kept in a read-only directory.

  • Use InitialWorkDirRequirement to stage input files in the working directory.