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Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows - #13335

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beatrizsavinhas wants to merge 69 commits into

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merge-bam-somatic-variant-calling-gatk

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Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows#13335
beatrizsavinhas wants to merge 69 commits into
masterfrom
merge-bam-somatic-variant-calling-gatk

Commits on Oct 16, 2026
- Remove BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK.
  beatrizsavinhas
  committed
  826fcda
- Merge logic until GATK4_GETPILEUPSUMMARIES.
  beatrizsavinhas
  committed
  9fc036e
Commits on Oct 19, 2026
- refactor using val_tumor_normal_analysis
  beatrizsavinhas
  committed
  a1ec7a3
Commits on Oct 20, 2026
- Fix channel manipulation and ensure case_id meta.
  beatrizsavinhas
  committed
  16e173f
- Add val_case_id.
  beatrizsavinhas
  committed
  4eb6294
- Add val_case_id.
  beatrizsavinhas
  committed
  844e870
- Re-add pileup output to test snapshot.
  beatrizsavinhas
  committed
  c0c19df
- Restore config to ensure generation of f1r2 file.
  beatrizsavinhas
  committed
  ac3c66d
Commits on Oct 21, 2026
- Code formatting.
  beatrizsavinhas
  committed
  77b171e
- Adjustments for tumor only mode.
  beatrizsavinhas
  committed
  d105449
- Remove val_case_id.
  beatrizsavinhas
  committed
  0c30792
- Fix code comments.
  beatrizsavinhas
  committed
  b2a414c
- Activate all tests and update snapshot.
  beatrizsavinhas
  committed
  f46df8b
- Remove logic for pileup_table_normal from emit block.
  beatrizsavinhas
  committed
  d1f9ba8
- Remove code duplication in output channels.
  beatrizsavinhas
  committed
  f3ecfe3
- Update code comment.
  beatrizsavinhas
  committed
  63f5038
- Update meta.
  beatrizsavinhas
  committed
  6b611f8
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  97d7543
- Rename folder.
  beatrizsavinhas
  committed
  c370a53
- Fix linting issue in meta.
  beatrizsavinhas
  committed
  2efdf20
- Run prek.
  beatrizsavinhas
  committed
  ea4e199
- Add pon to TO test.
  beatrizsavinhas
  committed
  d61ce99
- Remove case_id from test meta.
  beatrizsavinhas
  committed
  feb020a
- Create params.ext_args_gatk4_mutect2
  beatrizsavinhas
  committed
  b982828
- Add params.ext_args_gatk4_mutect2 for TO test. Fix bug with ext_args_gatk4_mutect2.
  beatrizsavinhas
  committed
  035822a
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  ddd5c28
Commits on Oct 22, 2026
Commits on Oct 23, 2026
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  b12965f
- Fix snapshot of pileup_table for TN test.
  beatrizsavinhas
  committed
  0838c54
- Update meta.
  beatrizsavinhas
  committed
  b6e7ae7
- Correct inputs for tumor only tests.
  beatrizsavinhas
  committed
  3fac4e1
- Update TN test snapshot based on CI results.
  beatrizsavinhas
  committed
  a7148d0
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  8b4d48a
- Update TN test snapshot based on CI results.
  beatrizsavinhas
  committed
  ae1894d
- Remove negation in if logic.
  beatrizsavinhas
  committed
  820a640
Commits on Oct 26, 2026
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  2de169d
- Apply suggestion from @imsarath
  
  beatrizsavinhas
  and
  imsarath
  authored
  c8a9b23
- Apply suggestion from @imsarath
  
  beatrizsavinhas
  and
  imsarath
  authored
  2241298
- Restore config.
  beatrizsavinhas
  committed
  c1df60c
- Add `sanitizeOutput` to stub tests.
  
  beatrizsavinhas
  and
  imsarath
  authored
  e9d93b9
- Deprecate BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK.
  beatrizsavinhas
  committed
  5085785
- Deprecate BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK.
  beatrizsavinhas
  committed
  c8784a9
- Deprecate BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK.
  beatrizsavinhas
  committed
  5308216
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  7010b29
- Remove assert workflow.success from deprecated subworkflow tests.
  beatrizsavinhas
  committed
  3c66880
- Fix deprecation_message for BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK.
  beatrizsavinhas
  committed
  6cdf452
- Add README for bam_tumor_only_somatic_variant_calling_gatk
  beatrizsavinhas
  committed
  a4918ee
- Add README for bam_tumor_normal_somatic_variant_calling_gatk
  beatrizsavinhas
  committed
  1238a97
- Restore BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK and fix deprecation.
  beatrizsavinhas
  committed
  81a78e5
- Restore BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK and fix deprecation.
  beatrizsavinhas
  committed
  5eadc6d
- Restore meta.
  beatrizsavinhas
  committed
  a0e36ef
Commits on Oct 29, 2026
Commits on Oct 30, 2026
Commits on Nov 2, 2026
- Improve meta manipulation code comment.
  beatrizsavinhas
  committed
  302bbec
- Improve meta manipulation code comment.
  beatrizsavinhas
  committed
  7aeb29f
- Merge branch 'master' into merge-bam-somatic-variant-calling-gatk
  beatrizsavinhas
  authored
  3b6bff3

Commits

Commits on Oct 16, 2026

Commits on Oct 19, 2026

Commits on Oct 20, 2026

Commits on Oct 21, 2026

Commits on Oct 22, 2026

Commits on Oct 23, 2026

Commits on Oct 26, 2026

Commits on Oct 29, 2026

Commits on Oct 30, 2026

Commits on Nov 2, 2026