All pull requests

Pull requests

• fix: list checksums.sha256 in the SKILL template's reproducibility tree

  #704·camlloyd opened Oct 25, 2026Collaborator·4 of 6 tasks·

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• chore: update site stats and skills catalog (automated)

  #703·manuelcorpas opened Oct 25, 2026Contributor·4 of 6 tasks·

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  1

• nf-core wrappers: leave samplesheet, reference-path and version checks to nf-core

  #702·danilomonge opened Oct 24, 2026Contributor·6 tasks done·

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  15

• ci(sweep): fail when a demo drops the reproducibility bundle

  audit:needs-review
  #684·camlloyd opened Oct 21, 2026Collaborator·4 of 6 tasks·

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  1

• multiomics-locus-integrator skill

  audit:needs-review
  #678·Adeel3Dgenomics opened Oct 20, 2026·6 tasks done·

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  1

• fix(wgs-prs): declare contigs and FORMAT fields in demo VCF and sort its records

  audit:safe
  #677·ShryukGrandhi opened Oct 20, 2026·4 of 6 tasks·

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  1

  1

• build(deps): bump github/codeql-action/analyze from 4.38.2 to 4.38.3

  audit:needs-reviewdependenciesgithub_actions
  #672·dependabot[bot] opened Oct 19, 2026Bot·

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  1

• build(deps): bump github/codeql-action/init from 4.38.2 to 4.38.3

  audit:needs-reviewdependenciesgithub_actions
  #670·dependabot[bot] opened Oct 19, 2026Bot·

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  1

• fix(methylation-clock): harden inputs and add synthetic demo

  audit:needs-review
  #661·dalloliogm opened Oct 19, 2026Contributor·

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  2

• Add snp-phewas: variant PheWAS across Pan-UK Biobank, FinnGen and the Million Veteran Program with nulls, one effect allele and replication verdicts

  audit:needs-review
  #659·madaraviv opened Oct 19, 2026Contributor·6 tasks done·

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  35

• fix(audit): say why a skill run failed in its span

  audit:needs-review
  #657·camlloyd opened Oct 18, 2026Collaborator·4 of 6 tasks·

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  1

• chore: drop Python 3.11, test on 3.14

  audit:needs-review
  #655·camlloyd opened Oct 18, 2026Collaborator·6 tasks done·

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  1

• fix(makefile): drop lint target whose script was deleted

  audit:needs-review
  #652·camlloyd opened Oct 17, 2026Collaborator·4 of 6 tasks·

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  1

• fix: update clinical-trial-finder examples to shared reproducibility layout — closes #630

  audit:needs-review
  #650·sooraj-codes opened Oct 16, 2026Contributor·

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  1

  3

• ci: test every skill on a schedule, and only affected skills on a PR

  audit:needs-review
  #640·camlloyd opened Oct 16, 2026Collaborator·4 of 6 tasks·

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  1

• fix(scrna-orchestrator): install scrublet and celltypist in a scrna extra; skip their tests without it

  audit:needs-review
  #632·camlloyd opened Oct 15, 2026Collaborator·6 tasks done·

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  1

• Consolidate nf-core wrappers on shared mechanics, strict validation and reliable replay

  audit:needs-review
  #623·danilomonge opened Oct 14, 2026Contributor·6 tasks done·

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  31

• test: reject an inconsistent homepage (count consistency gate)

  #615·manuelcorpas opened Oct 14, 2026Contributor·4 of 6 tasks·

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  1

• locuscompare: ask an assistant for the plot from an Open Targets page; honest labels; LD fix for leads whose ALT sorts before REF (0.3.0)

  audit:needs-reviewaudit:safe
  #604·madaraviv opened Oct 13, 2026Contributor·

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  4

• fix(pharmgx-reporter): DPYD Intermediate or Poor, not Indeterminate, when a reduced-function allele is detected and HapB3 is untested

  #603·manuelcorpas opened Oct 13, 2026Contributor·5 tasks done·

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  1

  7

• pharmgx-reporter: MTHFR informational only, methotrexate not graded on MTHFR (#594)

  audit:needs-reviewaudit:safe
  #599·abotescu20-maker opened Oct 12, 2026Contributor·

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  20

• feat(metagenome-mag-pipeline): shotgun metagenomics QC, assembly, binning and MAG assessment skill

  audit:needs-reviewaudit:security-review-required
  #544·mobashirrahman opened Oct 6, 2026·5 tasks done·

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  10

• feat(scrna-embedding-audit): score obsm embeddings against an in-run PCA baseline

  audit:safe
  #542·krudo-taco opened Oct 5, 2026Contributor·5 tasks done·

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  1

  5

• feat(isolate-amr-typing): MLST, AMR genotype and plasmid replicons for one bacterial isolate

  audit:needs-review
  #540·mobashirrahman opened Oct 5, 2026·5 tasks done·

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  17

• Add curated OpenAI research plugin packaging and offline demos

  #534·manuelcorpas opened Oct 5, 2026Contributor·5 tasks done·

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  9