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Sarek bcftools normalization#1682

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Patricie34 wants to merge 66 commits intonf-core:devnf-core/sarek:devfrom Patricie34:sarek_bcftools_normPatricie34/sarek:sarek_bcftools_normCopy head branch name to clipboard

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Commits on Apr 25, 2024

• First modification to contribute to the bcftools/norm module in Sarek

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• Changes in the GERMLINE_VCFS_NORM process

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• Add fasta argument to POST_VARIANTCALLING process.

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• add fasta input as argument

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• remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_vcfs_with_tbis and fasta.

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• First modification to contribute to the bcftools/norm module in Sarek

  JC-Delmas

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• Changes in the GERMLINE_VCFS_NORM process

  JC-Delmas

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• Add fasta argument to POST_VARIANTCALLING process.

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• add fasta input as argument

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• remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_vcfs_with_tbis and fasta.

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• Update workflows/sarek/main.nf

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Commits on Apr 30, 2024

• Resolved merge conflict by keeping changes from branch 34bf47b

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• Refactor normalization and concatenation of VCF files

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Commits on May 16, 2024

• Modify and adjust two scripts to add normalization and integrate FASTA support

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Commits on Oct 9, 2024

• Added normalization for all vcfs

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Commits on Oct 11, 2024

• Fixed linting issues and updated schema parameters

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• Update conf/modules/post_variant_calling.config

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• edit of normalization steps

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Commits on Oct 15, 2024

• Fixed linting issues

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• Merge remote-tracking branch 'upstream/dev' into sarek_bcftools_norm

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• Sync with dev_branch

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• Updated CHANGELOG.md

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Commits on Oct 16, 2024

• Update conf/modules/post_variant_calling.config

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  FriederikeHanssen

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• Update nextflow.config

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• Changed module.config

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• Changelog.md updated

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• Fixed params.normalize

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Commits on Oct 18, 2024

• Update CHANGELOG.md

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• pytesttags.yml changed

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• edited test_normalize_vcfs.yml

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Commits on Oct 22, 2024

• Separated vcf_normalization

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Commits on Nov 4, 2024

• Merge branch 'dev' into sarek_bcftools_norm

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Commits on Nov 5, 2024

• module.config edited

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• extra file removed

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• post_variantcalling edited

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• added annotation for vcfs_normalized

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Commits on Nov 19, 2024

• post_variant_calling.config changed

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• Merge branch 'dev' into sarek_bcftools_norm

  maxulysse

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Commits on Nov 20, 2024

• Update CHANGELOG.md

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• Update tests/test_normalize_vcfs.yml

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• Update tests/test_concat_germline_vcfs.yml

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• Merge remote-tracking branch 'upstream/dev' into sarek_bcftools_norm

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• CHANGELOG.md

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• Merge branch 'sarek_bcftools_norm' of github.com:Patricie34/sarek into sarek_bcftools_norm

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• test_normalize_vcfs.yml changed

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Commits on Nov 25, 2024

• Update conf/modules/post_variant_calling.config

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• Update subworkflows/local/vcf_normalization/main.nf

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• Update subworkflows/local/vcf_normalization/main.nf

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Commits on Nov 26, 2024

• versions corrected

  Patricie34

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Commits on Nov 27, 2024

• Apply suggestions from code review

  maxulysse

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• vcf_concatenate_germline workflow edit

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Commits on Nov 28, 2024

• major changes in concatenate_vcfs

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• paths in test.yml changed

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• linting changed

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• test_concatenate.yml edited

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• test_concatenate.yml edited

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• test_concatenate.yml adn normalize_yml edited

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Commits on Dec 4, 2024

• update docs, changelog and readme

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• output.md linting

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Commits on Dec 11, 2024

• subway_map updated

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Commits on Dec 17, 2024

• Resolved merge conflicts with upstream/dev

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• Subway_map updated

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Commits on Dec 18, 2024

• Merge remote-tracking branch 'upstream/dev' into sarek_bcftools_norm to update the latest changes.

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• CHANGELOG.md updated

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• CHANGELOG edited

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Commits on Jan 8, 2025

• README.md edited

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