Correct namespaces

[stain]

Correcting namespaces in the annotations:

• Correct namespaces for sbg so we don't get https://sevenbridges.comAWSInstanceType
• Add namespace for foaf and dct where missing

There are still some other warnings from cwltool:

(base) stain@biggie:~/src/topmed-workflows$ cwltool --print-rdf ./aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl  > file
INFO /home/stain/miniconda3/bin/cwltool 1.0.20190815141648
INFO Resolved './aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl' to 'file:///home/stain/src/topmed-workflows/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl'
vi file
INFO aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl:98:3: Unknown hint https://sevenbridges.com/AWSInstanceType
INFO aligner/sbg-alignment-cwl/topmed-alignment.cwl:160:3: Unknown hint https://sevenbridges.com/maxNumberOfParallelInstances
INFO aligner/sbg-alignment-cwl/steps/pre-align.cwl:164:3: Unknown hint https://sevenbridges.com/AWSInstanceType
INFO aligner/sbg-alignment-cwl/steps/align.cwl:202:3: Unknown hint https://sevenbridges.com/AWSInstanceType
INFO aligner/sbg-alignment-cwl/steps/samtools-sort.cwl:105:3: Unknown hint https://sevenbridges.com/AWSInstanceType
INFO aligner/sbg-alignment-cwl/steps/post-align.cwl:129:3: Unknown hint https://sevenbridges.com/AWSInstanceType
WARNING Workflow checker warning:
aligner/sbg-alignment-cwl/topmed-alignment.cwl:126:9: Source 'output' of type {"type": "array",
                                                      "items": ["null", "File"]} may be incompatible
aligner/sbg-alignment-cwl/topmed-alignment.cwl:140:9:   with sink 'alignment_files' of type
                                                        {"type": "array", "items": "File"}
aligner/sbg-alignment-cwl/topmed-alignment.cwl:102:9: Source 'cram' of type {"type": "array",
                                                      "items": ["null", "File"]} may be incompatible
aligner/sbg-alignment-cwl/topmed-alignment.cwl:114:9:   with sink 'input_file' of type {"type":
                                                        "array", "items": "File"}
aligner/sbg-alignment-cwl/topmed-alignment.cwl:81:9:  Source 'fastq' of type ["null", {"type":
                                                      "array", "items": "File"}] may be incompatible
aligner/sbg-alignment-cwl/topmed-alignment.cwl:91:9:    with sink 'fastq' of type {"type":
                                                        "array", "items": "File"}
aligner/sbg-alignment-cwl/topmed-alignment.cwl:82:9:  Source 'list' of type ["null", "File"] may be
                                                      incompatible
aligner/sbg-alignment-cwl/topmed-alignment.cwl:93:9:    with sink 'list' of type "File"
WARNING Workflow checker warning:
aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl:77:9: Source 'output' of type ["null",
                                                             "File"] may be incompatible
aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl:84:9:   with sink 'cram' of type "File"

[stain]

There is a different bug inside the CWL Viewer which freaks out over the id field (The w3id permalinks get wrong as they only handle those in the case of MULTIPLE workflows). Disabling the top-level id means it renders: https://view.commonwl.org/workflows/github.com/stain/topmed-workflows/blob/no-id/aligner/sbg-alignment-cwl/topmed-alignment.cwl