Code

Develop#37

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Merged

sroener merged 56 commits intomainkircherlab/cfDNA-UniFlow:mainfrom developkircherlab/cfDNA-UniFlow:developCopy head branch name to clipboardOct 23, 2023

+22,412-194

Commits

Commits on Aug 18, 2023

• refactor: minor textual changes

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  0c3f03c

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• feat: overhaul support for single end sequencing

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• refactor: update environment

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• feat: add signal extration around target regions; add GC correction overlay plots

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• feat: add case-control plots

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• refactor: update QC wrappers

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• fix: fix small format error

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• feat: add region data validation

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• refactor: update json schema version

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  2c8e6fb

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• fix: correct wrong validation schema

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• refactor: snakefmt

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Commits on Sep 6, 2023

• feat: new report sections

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• feat: add new plots to report cartegories

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• feat: add options for y-axis min range; refactor

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Commits on Sep 26, 2023

• refactor: clarify descriptions

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• refactor: change default figsize to (12,9)

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• perf: optimize data types during data loading

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• perf: optimize memory usage in SavGol filter application

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• perf: optimize data types during data loading

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• perf: optimize memory usage in SavGol filter application

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  f6cc864

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• style: multiple style fixes

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• fix: catch KeyError in chromosome mapping

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• feat: set min lower and upper limits for Y axis of plots

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  c1f3f85

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• refactor: optimize plotting for report

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Commits on Sep 28, 2023

• fix: remove name duplication in plot legend

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• feat: add more extensive figure description

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• feat: add more extensive figure description

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  5a4a772

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• feat: add more extensive figure description

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  c84a463

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• style: increase readability

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Commits on Oct 16, 2023

• perf: update GC correction to optimized version

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• refactor: pin version numbers

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• refactor: set phred-quality-encoding default to phred 33

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• test: add testregions for integration test

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• test: correct path to test regions

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• refactor: whitelist testregions

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• initial commit

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• test: test case hg38

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Commits on Oct 17, 2023

• refactor: consistent logging

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• doc: update abstract

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• doc: update overview figure

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• doc: generalize paths

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• doc: restructure documentation

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Commits on Oct 18, 2023

• feat: disable absolute paths in multiQC reportM

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• refactor: improve labeling of QC report

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• refactor: improve logging

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• fix: multiqc wrapper now uses provided files only

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• refactor: update example report

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• doc: add figures

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• doc: fix figure

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Commits on Oct 19, 2023

• refactor: spacing

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• doc: increase readability with background and font color

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Commits on Oct 23, 2023

• refactor: update GCbias plot

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• doc: update GC bias plots

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• feat: add option for normalized spline interpolation

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• refactor: style format with snakefmt

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• Merge branch 'main' into develop

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