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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snappy_wrappers/simple_wrapper.py Outdated Show resolved Hide resolved
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coveralls commented Dec 13, 2024 •
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Coverage Status

coverage: 85.855% (+0.09%) from 85.77%
when pulling ba3ea51 on 573-revamp-somatic-sv-calling-purityploidy-estimation
into 42d2c01 on main.

ErikaZ95 and others added 14 commits December 17, 2024 15:14
@ErikaZ95 @tedil
feat: Add snakemake parameter --ignore-incomplete to snappy-pipeline (#…
dbeb3ed 
…586)

Co-authored-by: Erika Zuljan <[email protected]>
Co-authored-by: Till Hartmann <[email protected]>
@ericblanc20
feat: clean-up manta. TODO: enable exome & rna
5036b7d
@ericblanc20
feat: initial implementation of a simple wrapper class for all snappy…
3958c8b 
… wrappers
@ericblanc20
refactor: complete re-write of ASCAT support
82109a9
@ericblanc20
--amend
ba593ea
@ericblanc20
style: use getattr for attributes
3c7b9bd
@ericblanc20
refactor: abstract wrapper, common models & generic ignore_chroms
48f98cf
@ericblanc20
refactor: use SnappyWrapper rather than SimpleWrapper
56e0159
@ericblanc20
docs: correct misleading comment
9555dfc
@ericblanc20
refactor: merged SimpleWrapper into SnappyWrapper
3363996
@ericblanc20
refactor: proper naming of wrapper scripts for logs
ba3ea51
@ericblanc20
refactor: sample sheets to pandas dataframe
dbadee4
@ericblanc20
feat: Add basic guess_sex step, required for CNV
5f532a4
@ericblanc20
refactor: adapt ascat to use the new guess_sex step
fd714d6
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revamp somatic sv calling & purity/ploidy estimation
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@tedil @coveralls @ericblanc20 @ErikaZ95