Issues

• Add a GERP BigWig parameter for VEP LOFTEE

  enhancement
  nf-core/sarek#2295 · Filter by author Joaodemeirelles opened on Oct 1, 2026

• bcftools mpileup: No such variable: intervals

  bug
  nf-core/sarek#2294 · Filter by author nikostr opened on Sep 30, 2026
  1

• GATK processes pull a ~2 GB gatk4_gcnvkernel image even when they don't use gcnvkernel

  nf-core/sarek#2291 · Filter by author pditommaso opened on Sep 25, 2026

• iGenomes URLs of test profile outdated

  bug
  nf-core/sarek#2290 · Filter by author JosuaCarl opened on Sep 25, 2026
  4

• Many URLs resolve with double //

  bug
  nf-core/sarek#2289 · Filter by author JosuaCarl opened on Sep 25, 2026

• FilterVariantTranches fails with "inconsistent references for the same position" when processing HaplotypeCaller WES data on GRCh37

  bug
  nf-core/sarek#2286 · Filter by author mrpribeiro opened on Sep 22, 2026

• GATK4_GATHERPILEUPSUMMARIES concatenates scattered pileup tables out of genome order

  bug
  nf-core/sarek#2281 · Filter by author Hope2925 opened on Aug 31, 2026

• BAM_MARKDUPLICATES emits duplicate alignment channel under -stub

  nf-core/sarek#2280 · Filter by author gburnett-nvidia opened on Aug 31, 2026

• fgbio GroupReadsByUmi crashes due to missing MQ tag

  bug
  nf-core/sarek#2279 · Filter by author sima-r opened on Aug 27, 2026

• ControlFreec pipeline does not run

  bug
  nf-core/sarek#2278 · Filter by author nicolas-source opened on Aug 25, 2026
  2

• Generated variantcalled.csv from Strelka Sarek run rejected for anotation step with vep

  bug
  nf-core/sarek#2276 · Filter by author AbhinavPraveen opened on Aug 25, 2026

• no_intervals = true conflicts with aligner = parabricks

  bug
  nf-core/sarek#2274 · Filter by author cariaso opened on Aug 19, 2026

• CNVkit and TIDDIT process only the first sample when multiple samples share a calling category

  nf-core/sarek#2273 · Filter by author FriederikeHanssen opened on Aug 19, 2026

• Support gVCF output and joint germline calling for Parabricks HaplotypeCaller

  enhancement
  nf-core/sarek#2261 · Filter by author FriederikeHanssen opened on Aug 7, 2026
  1

• Sentieon doesn't work when using Seqera Platform and a license server

  bug
  nf-core/sarek#2256 · Filter by author SPPearce opened on Aug 3, 2026
  3

• bwa-mem2.avx2 crashes (SIGSEGV) on Intel Core Ultra (Arrow Lake) under WSL2 — workaround: force SSE4.2 binary

  bug
  nf-core/sarek#2254 · Filter by author pn-pierre-joubert opened on Jul 31, 2026
  1

• Somatic tumor-normal run with indexcov fails at SAMTOOLS_REINDEX_BAM due to tuple mismatch

  bug
  nf-core/sarek#2251 · Filter by author lucafagnocchi opened on Jul 28, 2026

• Add GATK like filtering to Parabricks Haplotypecaller path

  enhancement
  nf-core/sarek#2250 · Filter by author FriederikeHanssen opened on Jul 28, 2026

• varlociraptor error during "MERGE_GERMLINE_SOMATIC_VCFS"

  nf-core/sarek#2231 · Filter by author ahwanpandey opened on Jul 13, 2026
  7

• varlociraptor custom scenario parameter issue

  nf-core/sarek#2230 · Filter by author ahwanpandey opened on Jul 10, 2026
  3

• Reuse of intervals-files

  enhancement
  nf-core/sarek#2226 · Filter by author asp8200 opened on Jul 1, 2026
  1

• MUSE channel cardinality

  nf-core/sarek#2224 · Filter by author FriederikeHanssen opened on Jun 29, 2026

• Update vars to secrets in awsmegatest action

  nf-core/sarek#2223 · Filter by author FriederikeHanssen opened on Jun 29, 2026

• Allow bam output for parabricks path

  nf-core/sarek#2222 · Filter by author FriederikeHanssen opened on Jun 29, 2026

• Tech Debt: Consolidate = vs set usage

  nf-core/sarek#2212 · Filter by author FriederikeHanssen opened on Jun 15, 2026