Enhance tests: run the resulting CWL description using test data

[mr-c]

• bowtie.cwl
• bcftools_stats
• bcftools_annotate
• CollectQualityYieldMetrics.cwl
• CollectReadgroupBamQualityMetrics.cwl
• deepvariant.cwl
• gatk.cwl
• hisat2.cwl
• isoseq3.cwl
• pbmm2.cwl
• read_string_cornercase.cwl
• rtg.cwl
• seqtk.cwl
• smoove.cwl
• transcriptclean_1.cwl
• TrimAdapters.cwl
• UmiCorrection.cwl
• validateOptimus_1.cwl
• validateOptimus_2.cwl
• validateOptimus_3.cwl
• validateOptimus_4.cwl
• validateOptimus_5.cwl
• vardict.cwl
• vt.cwl

and compare checksums to results from the source WDL files

[mr-c]

The framework to do this was introduced in be46678

The test files, if small, go in https://github.com/common-workflow-lab/wdl-cwl-translator/tree/main/wdl2cwl/tests/inputs

Each test is added to https://github.com/common-workflow-lab/wdl-cwl-translator/blob/main/wdl2cwl/tests/cwl_tests.yaml

[kinow]

@Th3nn3ss I think we made some progress here? Could you check and update the check boxes above? Thanks!!!

[mr-c]

These checkboxes are for the execution of the resulting CWL files. I didn't write any additional tests, though we did run them using the new code. So there will not be any new boxes to check..