2.5. Additional Arguments and Parameters

Sometimes tools require additional command line options that don’t correspond exactly to input parameters.

In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, “javac” will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct “javac” to write the class file to the designated output directory instead.

arguments.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
label: Example trivial wrapper for Java 9 compiler
hints:
  DockerRequirement:
    dockerPull: openjdk:9.0.1-11-slim
baseCommand: javac
arguments: ["-d", $(runtime.outdir)]
inputs:
  src:
    type: File
    inputBinding:
      position: 1
outputs:
  classfile:
    type: File
    outputBinding:
      glob: "*.class"

arguments-job.yml

src:
  class: File
  path: Hello.java

Next, create a sample Java file to use with the command-line tool.

$ echo "public class Hello {}" > Hello.java

And now invoke cwltool providing the tool description and the input object on the command line:

$ cwltool arguments.cwl arguments-job.yml
INFO /opt/hostedtoolcache/Python/3.9.19/x64/bin/cwltool 3.1.20240508115724
INFO Resolved 'arguments.cwl' to 'file:///home/runner/work/user_guide/user_guide/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl'
INFO [job arguments.cwl] /tmp/432rrbxd$ docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/432rrbxd,target=/fmJbUe \
    --mount=type=bind,source=/tmp/9bxua1oa,target=/tmp \
    --mount=type=bind,source=/home/runner/work/user_guide/user_guide/src/_includes/cwl/additional-arguments-and-parameters/Hello.java,target=/var/lib/cwl/stg5d0bd2c2-e696-4f6f-9366-bc20fd68c4a7/Hello.java,readonly \
    --workdir=/fmJbUe \
    --read-only=true \
    --net=none \
    --user=1001:127 \
    --rm \
    --cidfile=/tmp/w64iztec/20240518114040-425274.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/fmJbUe \
    openjdk:9.0.1-11-slim \
    javac \
    -d \
    /fmJbUe \
    /var/lib/cwl/stg5d0bd2c2-e696-4f6f-9366-bc20fd68c4a7/Hello.java
INFO [job arguments.cwl] completed success
{
    "classfile": {
        "location": "file:///home/runner/work/user_guide/user_guide/src/_includes/cwl/additional-arguments-and-parameters/Hello.class",
        "basename": "Hello.class",
        "class": "File",
        "checksum": "sha1$fdb876b40ad9ebc7fee873212e02d5940588642e",
        "size": 184,
        "path": "/home/runner/work/user_guide/user_guide/src/_includes/cwl/additional-arguments-and-parameters/Hello.class"
    }
}INFO Final process status is success

Here we use the arguments field to add an additional argument to the command line that isn’t tied to a specific input parameter.

arguments: ["-d", $(runtime.outdir)]

This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The $(runtime.outdir) parameter is the path to the designated output directory. Other parameters include $(runtime.tmpdir), $(runtime.ram), $(runtime.cores), $(runtime.outdirSize), and $(runtime.tmpdirSize). See the Runtime Environment section of the CWL specification for details.