Update consistency checks to be fully in python.

Please fill in the appropriate checklist below (delete those which are not relevant). These are the most common things requested on pull requests.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors
• Docker images moved to production release and changed in pipeline
• Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #60 (closed)

/cc @ghenry @venkat.malladi

changed milestone to %FUTURE Version

added CI/CD To Do labels

Cleanly done!

Don't forget the merge request checklist... I think the only one you need to do is the CHANGELOG (I would put this in the Background section of 0.0.4_indev). DAG is also important, but you can skip it here since there is another merge request pending.

I remade the authentication files, so I'm resubmitted the CI which was failing because of expired authentication. Once you add to the CHANGELOG and the CI passes I'll merge.

approved this merge request

added 1 commit

• 2c675d13 - Add changelong.

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marked the checklist item This comment contains a description of changes (with reason) as completed

marked the checklist item If you've fixed a bug or added code that should be tested, add tests! as completed

marked the checklist item CHANGELOG.md is updated as completed

marked the checklist item *Close issue* as completed

Changelog updated.

@venkat.malladi your consistency test failed

=================================== FAILURES ===================================
______________________________ test_consistencySE ______________________________
    @pytest.mark.consistencySE
    def test_consistencySE():
        assert os.path.exists(os.path.join(
            test_output_path, 'SE_multiqc_data.json'))
    
        with open(os.path.join(
            test_output_path, 'SE_multiqc_data.json')) as f:
            assigned_reads_json = json.load(f)
>       assigned_reads = assigned_reads_json['report_general_stats_data'][0]['16-1ZX4']['Assigned']
E       KeyError: '16-1ZX4'
workflow/tests/test_consistency.py:21: KeyError

added 1 commit

• ded770b2 - Fix consistency check for where it is grabbing.

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Updated to fix key error

enabled an automatic merge when the pipeline for ded770b2 succeeds

=================================== FAILURES ===================================
______________________________ test_consistencySE ______________________________
    @pytest.mark.consistencySE
    def test_consistencySE():
        assert os.path.exists(os.path.join(
            test_output_path, 'SE_multiqc_data.json'))
    
        with open(os.path.join(
            test_output_path, 'SE_multiqc_data.json')) as f:
            assigned_reads_json = json.load(f)
>       assigned_reads = assigned_reads_json['report_general_stats_data'][3]['16-1ZX4']['Assigned']
E       KeyError: 'Assigned'
workflow/tests/test_consistency.py:21: KeyError

aborted the automatic merge because source branch was updated

added 1 commit

• 4a5ac4a9 - Fix parsing of json file.

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added 7 commits

• 4a5ac4a9...c54dec24 - 6 commits from branch develop
• 573ff53b - Merge branch 'develop' into '60-consistency_tests'

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enabled an automatic merge when the pipeline for 573ff53b succeeds

aborted the automatic merge because source branch was updated

added 1 commit

• c7178e06 - Fix spelling error

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enabled an automatic merge when the pipeline for c7178e06 succeeds

aborted the automatic merge because source branch was updated

added 1 commit

• 7950f38f - Fix number of reads that map.

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merged

mentioned in commit f232c58b