GeezerVison

Pull requests

• Use = instead of .tap{} for channel assignment

  #2420·FriederikeHanssen opened Nov 12, 2026Contributor·3 tasks done·

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• Share joint calling or filtering between Sentieon DnaScope and Haplotyper

  #2417·FriederikeHanssen opened Nov 12, 2026Contributor··4 of 5 tasks·

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• Pass HaplotypeCaller VCFs on unfiltered when there are no filter resources

  #2416·FriederikeHanssen opened Nov 12, 2026Contributor··5 tasks done·

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• Fix --joint_germline with both sentieon_dnascope and sentieon_haplotyper

  #2413·FriederikeHanssen opened Nov 12, 2026Contributor·

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• Make --tools and --skip_tools case-insensitive

  #2412·FriederikeHanssen opened Nov 12, 2026Contributor··

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• Pass --tools/--skip_tools into subworkflows via take: inputs

  #2411·FriederikeHanssen opened Nov 12, 2026Contributor··

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• Move --tools/--skip_tools ext.when gates from module configs into workflow code

  #2410·FriederikeHanssen opened Nov 12, 2026Contributor··

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• deepsomatic ffpe

  #2402·FriederikeHanssen opened Nov 11, 2026Contributor·11 tasks·

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• Make --tools and --skip_tools case-insensitive

  #2392·FriederikeHanssen opened Nov 9, 2026Contributor·

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• Fix Parabricks DeepVariant stub filename collision

  #2366·gburnett-nvidia opened Nov 3, 2026Contributor·

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

  #2362·asp8200 opened Nov 3, 2026Contributor·

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• Add tumour mutational burden calculation with pyTMB

  #2361·sriramdevadas opened Nov 2, 2026·10 tasks done·

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• Add joint germline calling and filtering to Parabricks HaplotypeCaller

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

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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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• 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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• 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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• 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, 2026Contributor·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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