snakemake 6.8.0 → CWL

From @sofiakarb

> The issue I am currenlty facing has to do with Snakemake (v:6.8.0) - cwltool (v:3.1.20210521105815).
More specifically, my Snakefile is the following:

```
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule workflow:
input:
input_file=HTTP.remote("remote_link", keep_local=True)
params:
channels=[0, 1, 2, 3, 4],
psd_output_file_name="psd.json",
output_file_name="output.png"
output:
output="output.png"
cwl:
"file:workflow.cwl"
```

> While executing ```snakemake -c 1```, I get an error related to cwltool :

```
INFO /../bin/cwltool 3.1.20210521105815
ERROR Workflow error, try again with --debug for more information:
Invalid job input record:
../../../../tmp/tmpw06vyrgf:1:2: the `input_file` field is not valid because
is not a dict
```
> This is because .yml file that holds the information about ```Class: File``` is skipped due to the fact that Snakemake only needs the Snakefile (in which all input, parameters, outputs and cwl workflow file are provided). I can see two solutions, one from Snakemake side, where I must specificly provide the Class:File in the input_file field, and the other solution having a way cwltool to not provide errors (maybe just a warning?)

> Thank you beforehand for your support.

_Originally posted by @sofiakarb in https://github.com/common-workflow-language/cwltool/issues/758#issuecomment-951760232_