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Coverage QC stats#80

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jeff-k wants to merge 13 commits intoiqbal-lab-org:masteriqbal-lab-org/clockwork:masterfrom jeff-k:coverage_qcjeff-k/clockwork:coverage_qcCopy head branch name to clipboard

+209-85

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Commits on Oct 16, 2020

• Clobber (and warn about) existing output directories instead of raising exception.

  jeff-k

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  f7f3089

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• pin openpyxl to 2.5.0, newer versions break tests

  jeff-k

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• QC: database migrations and function stubs for counting coverage at depth thresholds

  jeff-k

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• measure coverage for lower thresholds, implement samtools depth stats collection

  jeff-k

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Commits on Oct 21, 2020

• Fixes for depth stats, additional test

  jeff-k

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Commits on Nov 12, 2020

• fix sql syntax error from copy+pasting

  jeff-k

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• Merge branch 'clobber_output_dir' into coverage_qc

  jeff-k

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• Merge branch 'master' into coverage_qc

  martinghunt

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Commits on Nov 13, 2020

• Fix samtools_qc tests

  martinghunt

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• Fix db_test to have new QC depth stats

  martinghunt

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  dc63b73

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• Get nextflow_qc tests to pass

  martinghunt

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• Merge branch 'master' of github.com:martinghunt/clockwork into coverage_qc

  jeff-k

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• Merge branch 'coverage_qc' of github.com:martinghunt/clockwork into coverage_qc

  jeff-k

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