Enhance tests: run the resulting CWL description using test data

[mr-c]

• [ ] bowtie.cwl
• [x] bcftools_stats
• [x] bcftools_annotate
• [x] CollectQualityYieldMetrics.cwl
• [x] CollectReadgroupBamQualityMetrics.cwl
• [x] 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
• [x] 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 https://github.com/common-workflow-lab/wdl-cwl-translator/commit/be466780198cf7c4977fbc04cf0fc4d5c26a9c4f

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..