`Error collecting output` for array of secondaryFiles

I'm attempting to use `biobambam2` `bamtofastq` (wrapped in a docker) to split BAMs into an arbitrary number of paired end fastq files. (example pair: D1K4L.4_1.fq.gz & D1K4L.4_2.fq.gz ). The cwl is at
https://github.com/jeremiahsavage/biobambam_tool/blob/a698b96ceee6e448ba9155e545a429a93f8eed55/biobambam2_bamtofastq.cwl.yaml

When run with a test BAM, I get the follow error:

``` bash
(p2_cwl) ubuntu@compute001:~/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513$ cwltool --debug ~/cocleaning-cwl/tools/biobambam2_bamtofastq.cwl.yaml --input_bam C440.TCGA-IN-8462-01A-11D-2340-08.1.bam --uuid test
/home/ubuntu/.virtualenvs/p2_cwl/bin/cwltool 1.0.20160325210917
Parsed job order from command line: {
"db_cred_s3url": null,
"uuid": "test",
"s3cfg_path": null,
"input_bam": {
"path": "C440.TCGA-IN-8462-01A-11D-2340-08.1.bam",
"class": "File"
},
"id": "/home/ubuntu/cocleaning-cwl/tools/biobambam2_bamtofastq.cwl.yaml",
"job_order": null
}
[job 140175215645712] initializing from file:///home/ubuntu/cocleaning-cwl/tools/biobambam2_bamtofastq.cwl.yaml
[job 140175215645712] {
"db_cred_s3url": null,
"uuid": "test",
"s3cfg_path": null,
"input_bam": {
"path": "C440.TCGA-IN-8462-01A-11D-2340-08.1.bam",
"class": "File"
},
"job_order": null
}
[job 140175215645712] path mappings is {
"C440.TCGA-IN-8462-01A-11D-2340-08.1.bam": [
"/mnt/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam",
"/var/lib/cwl/job203960872_47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam"
]
}
[job 140175215645712] command line bindings is [
{
"position": [
-1000000,
0
],
"valueFrom": "/home/ubuntu/.virtualenvs/p3/bin/python"
},
{
"position": [
-1000000,
1
],
"valueFrom": "/home/ubuntu/.virtualenvs/p3/lib/python3.4/site-packages/biobambam_tool/main.py"
},
{
"position": [
-1000000,
2
],
"valueFrom": "--tool_name"
},
{
"position": [
-1000000,
3
],
"valueFrom": "bamtofastq"
},
{
"position": [
0,
"db_cred_s3url"
],
"prefix": "--db_cred_s3url",
"valueFrom": null
},
{
"position": [
0,
"input_bam"
],
"prefix": "--bam_path",
"valueFrom": {
"path": "/var/lib/cwl/job203960872_47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam",
"containerfs": true,
"class": "File"
}
},
{
"position": [
0,
"s3cfg_path"
],
"prefix": "--s3cfg_path",
"valueFrom": null
},
{
"position": [
0,
"uuid"
],
"prefix": "--uuid",
"valueFrom": "test"
}
]
[job 140175215645712] /mnt/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513$ docker run -i --volume=/mnt/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam:/var/lib/cwl/job203960872_47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam:ro --volume=/mnt/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513:/var/spool/cwl:rw --volume=/tmp/tmp15xeVh:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1000 --rm --env=TMPDIR=/tmp --env=PATH=/usr/local/bin/:/usr/bin:/bin quay.io/jeremiahsavage/biobambam_tool /home/ubuntu/.virtualenvs/p3/bin/python /home/ubuntu/.virtualenvs/p3/lib/python3.4/site-packages/biobambam_tool/main.py --tool_name bamtofastq --bam_path /var/lib/cwl/job203960872_47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam --uuid test
Error while running job: Error collecting output for parameter 'output_fastq': Output file path /mnt/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513/fastq/D1K4L.4_2.fq.gz must be within designated output directory (/var/spool/cwl) or an input file pass through.
[job 140175215645712] completed permanentFail
[job 140175215645712] {}
Final process status is permanentFail
[job 140175215645712] Removing temporary directory /tmp/tmp15xeVh
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
Traceback (most recent call last):
File "/home/ubuntu/.virtualenvs/p2_cwl/local/lib/python2.7/site-packages/cwltool/main.py", line 581, in main
eval_timeout=args.eval_timeout
File "/home/ubuntu/.virtualenvs/p2_cwl/local/lib/python2.7/site-packages/cwltool/main.py", line 183, in single_job_executor
raise workflow.WorkflowException("Process status is %s" % (final_status))
WorkflowException: Process status is ['permanentFail']
(p2_cwl) ubuntu@compute001:~/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0_513$

```