All pull requests

Pull requests

• Add --references datasheet input

  #2307·maxulysse opened Oct 8, 2026Member·

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• Add varnet

  #2303·kiranchari opened Oct 6, 2026·8 of 11 tasks·

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• Add configurable LOFTEE GERP BigWig input

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

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  8

• Varlociraptor: fix scenario parsing

  #2300·famosab opened Oct 5, 2026Contributor·11 tasks·

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• Add DeepSomatic somatic variant calling

  #2293·FriederikeHanssen opened Sep 29, 2026Contributor·3 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/2279

  #2288·verdra opened Sep 24, 2026·7 tasks done·

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  6

• Fix PARABRICKS_FQ2BAM running BQSR without indexed known-sites VCFs

  #2287·dltamayo opened Sep 22, 2026·5 of 6 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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• 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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• Add GPU-accelerated mutectcaller from Parabricks

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

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  · 3.11
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• Add xengsort contamination removal support

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

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• Fix FilterMutectCalls skipped without germline_resource

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

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• Revise ASCAT resource generation instructions

  #2135·CharlesARoy opened Feb 10, 2026·2 tasks done·

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  · 3.9.0
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• [DRAFT] Feature/ploidy support

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

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• update cnvkit to reflect bug fixes

  blocked
  #2051·bounlu opened Nov 11, 2025Contributor·

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• Add mutect2 force calling using '--alleles' flag

  #1952·jchchiu opened Aug 11, 2025·8 of 11 tasks·

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  16

• Make lane Column Optional in Samplesheet

  #1943·animesh opened Jul 21, 2025·

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• build: Set process arch for arm64

  #1888·edmundmiller opened May 6, 2025Contributor·

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