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feat: preparation for somatic cnv#590

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Commits on Jan 16, 2025

• feat: sample sheet to pandas table

  

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• feat: added helper step guess_sex

  

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• feat: Support for ignore_chroms

  

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• feat: conditional execution of md5 (for pipes) & revert to R instead of Rscript, for more verbose logs

  

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• feat: Added boilerplate support for bcftools wrappers, and for tumor to normal sample mapping

  

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• feat: Complete bcftools arguments, except for files & threads

  

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• feat: Added germline_snvs step

  

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• fix: tool as argument rather than instance variable

  

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• fix: ngs_library not index anymore

  

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• refactor: better naming of basic bcftools command wrappers

  

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• refactor: modifed default models (added ploidy, header lines, removed BAQ, changed skip on flags), protect against None model values, changed regions option name

  

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• feat: Added the step preparing vcf files for CNV tools

  

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• feat: enable germline_snvs & somatic_variants_for_cnv steps

  

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• style: Make ruff 0.9 happy: join strings

  

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• style: Make ruff 0.9 happy: reformat assertions

  

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• style: Make ruff 0.9 happy: changes in line lengths

  

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• style: make snakefmt 0.10.2 happy: increase indentation

  

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Commits on Jan 21, 2025

• Update snappy_pipeline/workflows/common/samplesheet.py

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• Update snappy_pipeline/workflows/somatic_variants_for_cnv/__init__.py

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Commits on Jan 22, 2025

• refactor: finds snappy installation root directory from any wrapper location

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• docs: Adds some background on how to use germline_variants & somatic_variants_for_cnv steps

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• refactor: create a generic bcftools model, and push the complete one aside (because it's not quite complete)

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• build: pin versions

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• refactor: sample sheets indexed by ngs library name

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• style: Nicer parameter definition, renamed last to remove_unseen, use workflow config attributes & removed unnecessary resource allocation

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• refactor: renamed 'last' action to 'remove_unseen'

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• refactor: use generic bcftools model

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• refactor: remove merge confict (in docstring)

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Commits on Feb 6, 2025

• fix: sub-step name copy-paste error fixed

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