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🚀 Add matched analyses #2

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wants to merge 15 commits into from
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🚀 Add matched analyses #2

wants to merge 15 commits into from

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juanesarango
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@juanesarango juanesarango commented Jan 23, 2024

Right now purple runs in unmatched tumor-only mode. This PRs adds:

  • Reference arguments for normals
  • Tests for matched and unmatched
    • Unit tests
    • End-2-end
  • Support to add snps and svs as inputs
    • Add Sage for somatic calling

@juanesarango juanesarango marked this pull request as draft August 14, 2024 20:59
@juanesarango juanesarango marked this pull request as ready for review December 21, 2024 08:36

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Copilot reviewed 38 out of 50 changed files in this pull request and generated no comments.

Files not reviewed (12)
  • main.nf: Language not supported
  • nextflow.config: Language not supported
  • nf-test.config: Language not supported
  • run.sh: Language not supported
  • run_sage.sh: Language not supported
  • tests/data/amber/TEST_TUMOR.amber.baf.pcf: Language not supported
  • tests/data/amber/TEST_TUMOR.amber.qc: Language not supported
  • tests/data/cobalt/TEST_NORMAL.cobalt.ratio.pcf: Language not supported
  • tests/data/cobalt/TEST_TUMOR.cobalt.ratio.pcf: Language not supported
  • tests/data/cobalt/binned_100_probes_0.5_LogR/TEST_NORMAL.cobalt.ratio.pcf: Language not supported
  • tests/data/cobalt/binned_100_probes_0.5_LogR/TEST_TUMOR.cobalt.ratio.pcf: Language not supported
  • tests/data/ref/ensembl_data/ensembl_gene_data.csv: Language not supported
@juanesarango
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Closing in favor of #4

@juanesarango juanesarango deleted the run-matched branch December 24, 2024 05:43
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