Symlinking input to docker on Mac links in local, not the host VM

I am trying to run cwltool on Mac that invokes a Docker container. When I specify the input to cwltool, in order for the container to access the input file cwltool is trying to create a symlink to the input file inside the host VM. But since I am running cwltool locally it creates the link locally instead, which causes the container to fail because it can't locate the input file inside the host.

Here is the command line I am using:

```
cwl-runner --debug samtools-workflow.cwl --input test/input/original.bam
```

and I end up with this symlink _in my local directory_:

```
indexed.bam -> test/input/original.bam
```

I end up with these lines in the debug output:

```
[job samindex] /var/folders/2l/0wpdpqws4jvg9lqjwrhvdcl8_c3ksp/T/tmpTvbsTy$ docker run -i --volume=/Users/spanglry/Code/pipelines-api-examples/samtools/test/input/original.bam:/var/lib/cwl/job956205074_input/original.bam:ro --volume=/var/folders/2l/0wpdpqws4jvg9lqjwrhvdcl8_c3ksp/T/tmpTvbsTy:/var/spool/cwl:rw --volume=/var/folders/2l/0wpdpqws4jvg9lqjwrhvdcl8_c3ksp/T/tmpYpwv0a:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1000 --rm --env=TMPDIR=/tmp sha256:f8de369e9dddf875c5f53c5aada66596d12affccf8b96da15a00c48a1b3a4be9 samtools index indexed.bam
symlinking /var/folders/2l/0wpdpqws4jvg9lqjwrhvdcl8_c3ksp/T/tmpTvbsTy/indexed.bam to /var/lib/cwl/job956205074_input/original.bam
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
```

Contents of samtools-workflow.cwl -----------------

```
#!/usr/bin/env cwl-runner

class: Workflow

inputs:
- id: "#input"
type: File
description: "bam file"

outputs:
- id: "#bam"
type: File
source: "#samindex.bam_with_bai"

hints:
- class: DockerRequirement
dockerLoad: gcr.io/level-elevator-714/samtools
dockerImageId: sha256:f8de369e9dddf875c5f53c5aada66596d12affccf8b96da15a00c48a1b3a4be9

steps:
- id: "#samindex"
run: { import: samtools-index.cwl }
inputs:
- { id: "#samindex.input", source: "#input" }
outputs:
- { id: "#samindex.bam_with_bai" }
```

Contents of samtools-index.cwl -------------------

```
#!/usr/bin/env cwl-runner

class: CommandLineTool

description: "Invoke 'samtools index' to create a 'BAI' index (samtools 1.19)"

requirements:
- class: CreateFileRequirement
fileDef:
- filename: indexed.bam
fileContent:
engine: "cwl:JsonPointer"
script: "job/input"

inputs:
- id: "#input"
type: File
description:
Input bam file.

outputs:
- id: "#bam_with_bai"
type: File
outputBinding:
glob: "indexed.bam"
secondaryFiles:
- ".bai"

baseCommand: ["samtools", "index"]

arguments:
- "indexed.bam"
- "indexed.bam.bai"
```

Questions:

Is there some way to indicate I want to be symlinking the input inside the docker host instead of the process running the script?

Am I doing something else wrong here?

Any help would be greatly appreciated, thank you!