Add HTSLIB/BGZIPTABIX and deprecate redundant modules#11571

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itrujnara wants to merge 33 commits into

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itrujnara:tabixupdate

Commits on May 8, 2026

feat: update test snapshots and fix timestamp formatting in VCF annotation workflow
itrujnara
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feat: deprecate SAMTOOLS_BGZIP
itrujnara
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feat: Refactor and deprecate tabix module in favor of HTSLIB/BGZIPTABIX
itrujnara
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feat: update VCF processing workflows to improve output handling and metadata consistency
itrujnara
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Merge branch 'master' into tabixupdate
itrujnara
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feat: update tabix command logic and add test for VCF compression with index
itrujnara
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feat: update input file definitions and add optional regions file support in bgziptabix module
itrujnara
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Merge branch 'tabixupdate' of https://github.com/itrujnara/modules into tabixupdate
itrujnara
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feat: update output file definitions to use consistent naming for compressed files
itrujnara
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fix: Add missing module information in subworkflow meta.yml
itrujnara
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Merge branch 'master' into tabixupdate
itrujnara
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fix: update samtools version to 1.23.1 in environment.yml
itrujnara
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Merge branch 'tabixupdate' of https://github.com/itrujnara/modules into tabixupdate
itrujnara
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test: Update snapshot for bam_variant_calling_mpileup_bcftools
itrujnara
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fix: update container image and samtools version in PARAPHASE process
itrujnara
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fix (multivcfanalyzer): update htslib version to 1.23.1 and adjust test snapshots
itrujnara
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fix(paraphase): standardize quotes in gzip command for consistency
itrujnara
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Commits on May 11, 2026

Merge branch 'master' into tabixupdate
itrujnara
authored

Commits on May 13, 2026