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feat: revamp somatic sv calling purityploidy estimation #582

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feat: revamp somatic sv calling purityploidy estimation #582

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tedil
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@tedil tedil commented Dec 13, 2024

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@tedil tedil linked an issue Dec 13, 2024 that may be closed by this pull request
revamp somatic sv calling & purity/ploidy estimation #573
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  • Please format your Python code with ruff: make fmt
  • Please check your Python code with ruff: make check
  • Please format your Snakemake code with snakefmt: make snakefmt

You can trigger all lints locally by running make lint

tedil
tedil commented Dec 13, 2024
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If designed like this, wouldn't it make more sense to have a ShellWrapper and an RWrapper which inherit from the SimpleWrapper? That way, you could replace the run_bash and run_R methods with a single run method which is different for ShellWrapper and RWrapper

snappy_wrappers/simple_wrapper.py Outdated Show resolved Hide resolved
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Coverage Status

coverage: 85.683% (-0.09%) from 85.77%
when pulling 3431c5d on 573-revamp-somatic-sv-calling-purityploidy-estimation
into 42d2c01 on main.

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revamp somatic sv calling & purity/ploidy estimation
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