All pull requests

Pull requests

• Add joint germline calling and filtering to Parabricks HaplotypeCaller

  #2353·FriederikeHanssen opened Oct 29, 2026Contributor·8 tasks done·

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• Sort BED intervals in reference order before splitting them

  #2352·FriederikeHanssen opened Oct 29, 2026Contributor·5 tasks done·

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• Make Mosdepth fast mode configurable

  #2351·FriederikeHanssen opened Oct 29, 2026Contributor·5 of 7 tasks·

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• Filter Parabricks MutectCaller calls with GATK FilterMutectCalls

  #2349·FriederikeHanssen opened Oct 29, 2026Contributor·7 of 9 tasks·

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• Important! Template update for nf-core/tools v4.2.1

  #2345·nf-core-bot opened Oct 26, 2026Member·

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• Fix double slashes in test profile URLs

  #2341·filipetessaro opened Oct 25, 2026·4 of 6 tasks·

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• fix: reuse references for multi-sample CNVkit and TIDDIT calling

  #2340·Daesun-Ryu opened Oct 24, 2026·3 of 6 tasks·

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• Update parabricks modules to version 4.8

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

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

  #2333·verdra opened Oct 19, 2026·

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• 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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• [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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• chore(agents): install issue-graph skill

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

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

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

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• Fix validation for step annotate

  #2322·famosab opened Oct 15, 2026Member·1 of 11 tasks·

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• Add varnet

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

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• 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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• Apply workflow output syntax to reference and preprocessing outputs

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

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• 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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• 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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