All pull requests

Pull requests

• Run all nf-tests when a conf/modules config changes

  #2395·FriederikeHanssen opened Nov 10, 2026Contributor·1 of 3 tasks·

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

  #2392·FriederikeHanssen opened Nov 9, 2026Contributor·

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• Make lane column optional for single-row samples

  #2391·FriederikeHanssen opened Nov 9, 2026Contributor·1 task done·

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• Cf omit sex

  #2389·EladH1 opened Nov 9, 2026Contributor·6 of 13 tasks·

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• Release 3.12

  #2374·FriederikeHanssen opened Nov 5, 2026Contributor·11 tasks·

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  56

• 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 of 9 tasks·

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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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  25

• 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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