Code

feat: fusion calling#222

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Merged

johanneskoester merged 68 commits intomastersnakemake-workflows/dna-seq-varlociraptor:masterfrom fusion_callingsnakemake-workflows/dna-seq-varlociraptor:fusion_callingCopy head branch name to clipboardFeb 27, 2024

+861-227

Commits

Commits on Dec 15, 2022

• Initial commit

  FelixMoelder

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  210603c

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Commits on Dec 19, 2022

• concat arriba calls

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Commits on Jan 13, 2023

• generalize workflow

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Commits on Mar 16, 2023

• Merge branch 'master' into fusion_calling

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• update arriba

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• Update tests

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• typo

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Commits on May 10, 2023

• Merge branch 'master' into fusion_calling

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Commits on May 12, 2023

• intermediate changes

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  273fbdc

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• Merge branch 'fusion_calling' of github.com:snakemake-workflows/dna-seq-varlociraptor into fusion_calling

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  5a24102

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• remove repetetive code

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  0cb7f25

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• fix typo

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Commits on Aug 31, 2023

• indexing

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• Merge branch 'master' into fusion_calling

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• snakefmt

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Commits on Sep 6, 2023

• refactoring

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• fmt

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• fmt

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  0043a9f

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Commits on Sep 7, 2023

• fixed incompatibilities

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Commits on Sep 11, 2023

• skip vep

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Commits on Sep 12, 2023

• improve report

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  e1e9b62

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Commits on Sep 15, 2023

• Fix final output

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• fix output

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  d8e27f9

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• handle mutational burden

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  1357b44

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• remove unused rules, separate groups

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  e42caa2

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Commits on Sep 20, 2023

• fix minor issues

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  b0d24ec

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• cleanup

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• Add missing script

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  b3d574e

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Commits on Sep 21, 2023

• update readme

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Commits on Sep 22, 2023

• update freebayes

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  8f90131

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Commits on Oct 17, 2023

• reset download revel

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  333ae5e

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Commits on Oct 26, 2023

• Merge branch 'master' into fusion_calling

  FelixMoelder

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  289315a

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Commits on Oct 27, 2023

• renaming

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  91815b6

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• fix datatype handling

  FelixMoelder

  committed
  cdc8d2d

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• fmt

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  3e5a3ba

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• fmt

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  805df4d

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Commits on Nov 13, 2023

• merge master

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  1d8a179

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• Update wrapper

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  b968321

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Commits on Nov 29, 2023

• Merge branch 'master' into fusion_calling

  FelixMoelder

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  aa8d20a

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Commits on Nov 30, 2023

• Merge branch 'master' into fusion_calling

  FelixMoelder

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  251597d

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Commits on Dec 1, 2023

• Merge branch 'master' into fusion_calling

  FelixMoelder

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  b88a90c

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Commits on Dec 12, 2023

• breaking up workflow (not yet working)

  FelixMoelder

  committed
  dad77e0

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• Merge branch 'fusion_calling' of github.com:snakemake-workflows/dna-seq-varlociraptor into fusion_calling

  FelixMoelder

  committed
  721d5c9

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• fmt

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• fmt

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• fmt

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• Merge branch 'master' into fusion_calling

  FelixMoelder

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  2b48e51

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Commits on Jan 16, 2024

• invoked datatype and candidate-calling

  FelixMoelder

  committed
  d1e2383

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• fix formatting

  FelixMoelder

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  ada0627

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Commits on Jan 18, 2024

• unified workflow

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  c71aef4

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• formatting

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• update samplesheet

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• Add read group for star

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  479c144

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• fix param

  FelixMoelder

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  1bd1720

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Commits on Jan 19, 2024

• support fusions and variants in rna

  FelixMoelder

  committed
  0e4f5c1

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Commits on Jan 24, 2024

• feat: render canonical transcript source

  FelixMoelder

  committed
  d6f4a9c

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Commits on Jan 26, 2024

• clean report

  FelixMoelder

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Commits on Jan 29, 2024

• Merge remote-tracking branch 'origin/feat/render_canonical_source' into fusion_calling

  FelixMoelder

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Commits on Feb 13, 2024

• cleanup template

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• github action workaround

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Commits on Feb 15, 2024

• update readme

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  8e8e581

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Commits on Feb 26, 2024

• cleanup

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  c738abb

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• fmt

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  486722a

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• introduce pattern delegatoin

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• fmt

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• add comment to script

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  fca151c

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• typo

  FelixMoelder

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• Update convert_fusions_to_vcf.sh

  FelixMoelder

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