output at home folder and cp: cannot stat errors

[uui23]

Hi Yee
I have some issues when I want to use the sailor. and need your help.
I can use executable version, get results with example,
singularity run pathto/sailor-1.0.4 ce11_example.yaml
but the output at home/user folder rather the expected folder where I run the command.

when I use myself json/yaml file,
singularity run pathto/sailor-1.0.4 abspath(xx.json)
it raise

cp: cannot stat '/xtdisk/pujm/stamp/rnaseq/sailor/test/out/xx.json': No such file or directory
chmod: cannot access '/home/pujm/xx/SAILOR-JOB-COPY.xx.txt': No such file or directory
/opt/conda/bin/cwltool 1.0.20170413194156
Resolved '/opt/sailor/cwl/rnaediting2strands.workflow.cwl' to 'file:///opt/sailor/cwl/rnaediting2strands.workflow.cwl'
[Errno 2] No such file or directory: '/xtdisk/pujm/stamp/rnaseq/sailor/test/out/xx.json'
cp: cannot stat '/home/pujm/xx/.tmp/outdir/*': No such file or directory

singularity run pathto/sailor-1.0.4 xx.json
It raise

cp: cannot stat 'xx.json': No such file or directory
chmod: cannot access '/home/pujm/xx/SAILOR-JOB-COPY.xx.txt': No such file or directory
/opt/conda/bin/cwltool 1.0.20170413194156
Resolved '/opt/sailor/cwl/rnaediting2strands.workflow.cwl' to 'file:///opt/sailor/cwl/rnaediting2strands.workflow.cwl'
[Errno 2] No such file or directory: '/home/pujm/xx.json'
cp: cannot stat '/home/pujm/xx/.tmp/outdir/*': No such file or directory

But If I cp abspath(xx.json) or xx.json, it works well.
also, when I use your another example, it raise same cp stat error
singularity run pathto/sailor-1.0.4 example.json

cp: cannot stat 'example.json': No such file or directory
chmod: cannot access '/home/pujm/example/SAILOR-JOB-COPY.example.txt': No such file or directory
/opt/conda/bin/cwltool 1.0.20170413194156
Resolved '/opt/sailor/cwl/rnaediting2strands.workflow.cwl' to 'file:///opt/sailor/cwl/rnaediting2strands.workflow.cwl'
[Errno 2] No such file or directory: '/home/pujm/example.json'
cp: cannot stat '/home/pujm/example/.tmp/outdir/*': No such file or directory

I also found the 1.2.0 version
setup well, then I run
cwltool cwl/wf_rnaediting2strands.cwl example/ce11_example.yaml
Error raised

$cwltool cwl/wf_rnaediting2strands.cwl example/ce11_example.yaml
INFO /pnas/pujm/anaconda3/bin/cwltool 3.1.20211004060744
Traceback (most recent call last):
  File "/pnas/pujm/anaconda3/bin/cwltool", line 8, in <module>
    sys.exit(run())
  File "/pnas/pujm/anaconda3/lib/python3.7/site-packages/cwltool/main.py", line 1399, in run
    sys.exit(main(*args, **kwargs))
  File "/pnas/pujm/anaconda3/lib/python3.7/site-packages/cwltool/main.py", line 1002, in main
    fetcher_constructor=loadingContext.fetcher_constructor,
  File "/pnas/pujm/anaconda3/lib/python3.7/site-packages/cwltool/load_tool.py", line 98, in resolve_tool_uri
    raise ValidationException("Not found: '%s'" % argsworkflow)
schema_salad.exceptions.ValidationException: Not found: 'cwl/wf_rnaediting2strands.cwl'

So, which version should I use, if I want to find C to T mutation.
if I use executable 1.0.4 version how to output the reults at specified folder rather /home/user/.. and how to solve the cp: cannot stat error, I don't know whether these are myself errors or other one also encountered.
if use newest version 1.2.0, it contains lots of files, so how to use this in more detail?
Lastly, are json and yaml both can be input of sailor?
Thanks!