All pull requests

Pull requests

• Update parabricks modules to version 4.8

  #2339·gburnett-nvidia opened Oct 22, 2026Contributor·

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  4

• Runs samtools/fixmate after ALIGN_UMI when run with bwa-mem2

  #2333·verdra opened Oct 19, 2026·

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  2

• ci: trial manual full-size tests on the dev CPU environment

  #2330·edmundmiller opened Oct 17, 2026Contributor·3 of 6 tasks·

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  3

• [POC] Add nf-snapshot output check to the AWS full-size somatic test

  #2327·adamrtalbot opened Oct 15, 2026Contributor·2 of 4 tasks·

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  5

• chore(agents): install issue-graph skill

  #2325·edmundmiller opened Oct 15, 2026Contributor·1 of 3 tasks·

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  2

• feat(lint): warn when a workflow if could use a filter

  #2324·edmundmiller opened Oct 15, 2026Contributor·3 of 5 tasks·

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  3

• chore(lint): set up ast-grep for Nextflow with mise

  #2323·edmundmiller opened Oct 15, 2026Contributor·3 of 5 tasks·

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  3

• Fix validation for step annotate

  #2322·famosab opened Oct 15, 2026Member·11 tasks·

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  5

• Release 3.11.0

  #2313·famosab opened Oct 13, 2026Member·11 tasks·

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  19

• Add varnet

  #2311·kiranchari opened Oct 12, 2026·8 of 11 tasks·

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  4

• Add --references datasheet input

  #2307·maxulysse opened Oct 8, 2026Member·

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• Add configurable LOFTEE GERP BigWig input

  #2301·Joaodemeirelles opened Oct 5, 2026·5 of 6 tasks·

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  10

• Apply workflow output syntax to reference and preprocessing outputs

  #2292·FriederikeHanssen opened Sep 29, 2026Contributor·17 of 23 tasks·

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  3

• Fix support for intervals in list format (igenomes GATK.GRCh37 interval file)

  #2285·jchchiu opened Sep 21, 2026·4 of 11 tasks·

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  2

• fix(markduplicates): avoid duplicate alignment emission under -stub

  #2277·gburnett-nvidia opened Aug 25, 2026Contributor·2 tasks done·

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  10

• Require CPU stub topology tests

  #2267·FriederikeHanssen opened Aug 12, 2026Contributor·3 of 4 tasks·

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• Balance nf-test shards by runtime

  #2266·FriederikeHanssen opened Aug 12, 2026Contributor·3 of 4 tasks·

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• Collect nf-test runtime reports

  #2265·FriederikeHanssen opened Aug 12, 2026Contributor·3 of 5 tasks·

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• Bump nf schema 2.8.0

  #2263·rcannood opened Aug 11, 2026·3 of 6 tasks·

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• avoid misleading sample-sheet errors on unrelated pipeline abort (#1629)

  #2245·asp8200 opened Jul 22, 2026Contributor·

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• Refactor BQSR: route SV/CNV callers to markdup output (pre-BQSR)

  #2205·FriederikeHanssen opened Jun 9, 2026Contributor·3 tasks·

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  1

• Add GPU-accelerated mutectcaller from Parabricks

  #2180·gburnett-nvidia opened May 6, 2026Contributor·

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  · 3.11
  44

• Add xengsort contamination removal support

  #2161·famosab opened Mar 25, 2026Member·11 tasks done·

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  · 3.12
  26

  

• Fix FilterMutectCalls skipped without germline_resource

  #2153·FriederikeHanssen opened Mar 9, 2026Contributor·5 tasks·

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  2

• [DRAFT] Feature/ploidy support

  #2091·zhliUU opened Jan 12, 2026·4 of 15 tasks·

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