input string object conversion to filePath due to name "format"

[FarahZKhan]

Expected Behavior

job_order_object should save "format":"farlik2013" as a string object.

Actual Behavior

"format":"farlik2013" turns into "file:///path/to/current/directory/farlik2013"

Workflow Code

The code is on GitHub:
https://github.com/Epigenomics-Screw/Screw/blob/master/cwl/preprocess.cwl

Full Traceback

../TestProv/cwltool/cwltool.py 1.0.20180317064229
Resolved 'cwl/preprocess.cwl' to 'file:///Users/farahkhan/Documents/Screw/cwl/preprocess.cwl'
job order object in init_job_order!!!! ordereddict([('toConvert', ordereddict([('basename', 'GSM1589192_K562.1_2.txt.chr19'), ('nameroot', 'GSM1589192_K562.1_2.txt'), ('nameext', '.chr19'), ('location', 'file:///Users/farahkhan/Documents/Screw/test_data/GSM1589192_K562.1_2.txt.chr19'), ('class', 'File'), ('size', 2505689)])), ('format', 'file:///Users/farahkhan/Documents/Screw/farlik2013'), (u'id', 'file:///Users/farahkhan/Documents/Screw/example_job.json')])
job order object is!!!!!! ordereddict([('toConvert', ordereddict([('basename', 'GSM1589192_K562.1_2.txt.chr19'), ('nameroot', 'GSM1589192_K562.1_2.txt'), ('nameext', '.chr19'), ('location', 'file:///Users/farahkhan/Documents/Screw/test_data/GSM1589192_K562.1_2.txt.chr19'), ('class', 'File'), ('size', 2505689)])), ('format', 'file:///Users/farahkhan/Documents/Screw/farlik2013')])
[workflow preprocess.cwl] start
[workflow preprocess.cwl] starting step convertMethylation
[step convertMethylation] start
[job convertMethylation] /private/tmp/docker_tmp0hziZo$ docker \
    run \
    -i \
    --volume=/private/tmp/docker_tmp0hziZo:/private/var/spool/cwl:rw \
    --volume=/private/var/folders/tl/1j6jy66x3nvfbxt8ycs_q21m0000gn/T/tmpVBdIRM:/tmp:rw \
    --volume=/Users/farahkhan/Documents/Screw/test_data/GSM1589192_K562.1_2.txt.chr19:/private/var/lib/cwl/stg18f866b3-fbe8-4dea-b459-ca26b7fccd44/GSM1589192_K562.1_2.txt.chr19:ro \
    --workdir=/private/var/spool/cwl \
    --read-only=true \
    --user=501:20 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/private/var/spool/cwl \
    quay.io/epigenomic_screw/screw \
    interconverter.sh \
    -d \
    /private/var/spool/cwl \
    -f \
    file:///Users/farahkhan/Documents/Screw/farlik2013 \
    -i \
    /private/var/lib/cwl/stg18f866b3-fbe8-4dea-b459-ca26b7fccd44/GSM1589192_K562.1_2.txt.chr19
That format isn't recognised. Currently recognised are farlik2016, farlik2015, farlik2013, guo2013, smallwood2014
[job convertMethylation] Job error:
Error collecting output for parameter 'converted':
cwl/interconverter.cwl:26:7: Did not find output file with glob pattern: '['*.meth']'
[job convertMethylation] completed permanentFail
[step convertMethylation] Output is missing expected field file:///Users/farahkhan/Documents/Screw/cwl/preprocess.cwl#convertMethylation/converted
[step convertMethylation] completed permanentFail
[workflow preprocess.cwl] completed permanentFail
{
    "covBW": null, 
    "methBW": null, 
    "converted": null, 
    "combined": null
}
Final process status is permanentFail
End Time:  Sat, 17 Mar 2018 10:23:22 +0000

Your Environment

cwltool version: cwltool 1.0.20180227092251

This is most probably because of the name of the input parameter "format".