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Pull requests: nf-core/sarek

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Pull requests list

Fix PARABRICKS_FQ2BAM running BQSR without indexed known-sites VCFs
#2287 opened Sep 22, 2026 by dltamayo Loading…
5 of 6 tasks
Fix support for intervals in list format (igenomes GATK.GRCh37 interval file)
#2285 opened Sep 21, 2026 by jchchiu Loading…
4 of 11 tasks
2
Wire up gVCF output for Parabricks HaplotypeCaller
#2282 opened Aug 31, 2026 by gburnett-nvidia Contributor Loading…
3 tasks done
5
fix(markduplicates): avoid duplicate alignment emission under -stub
#2277 opened Aug 25, 2026 by gburnett-nvidia Contributor Loading…
2 tasks done
1
9
Require CPU stub topology tests
#2267 opened Aug 12, 2026 by FriederikeHanssen Contributor • Draft
3 of 4 tasks
1
Balance nf-test shards by runtime
#2266 opened Aug 12, 2026 by FriederikeHanssen Contributor • Draft
3 of 4 tasks
1
Collect nf-test runtime reports
#2265 opened Aug 12, 2026 by FriederikeHanssen Contributor • Draft
3 of 5 tasks
2
Bump nf schema 2.8.0
#2263 opened Aug 11, 2026 by rcannood • Draft
3 of 6 tasks
avoid misleading sample-sheet errors on unrelated pipeline abort (#1629)
#2245 opened Jul 22, 2026 by asp8200 Contributor Loading…
2
Refactor BQSR: route SV/CNV callers to markdup output (pre-BQSR)
#2205 opened Jun 9, 2026 by FriederikeHanssen Contributor • Draft
3 tasks
1
Add GPU-accelerated mutectcaller from Parabricks
#2180 opened May 6, 2026 by gburnett-nvidia Contributor Loading… 3.11
37
Add Parabricks (GPU-based) DeepVariant
#2177 opened Apr 29, 2026 by gburnett-nvidia Contributor Loading…
9 tasks done
3.11
46
Add xengsort contamination removal support
#2161 opened Mar 25, 2026 by famosab Contributor Loading…
11 tasks done
@xinghansun
2
Fix FilterMutectCalls skipped without germline_resource
#2153 opened Mar 9, 2026 by FriederikeHanssen Contributor Loading…
5 tasks
2
Revise ASCAT resource generation instructions
#2135 opened Feb 10, 2026 by CharlesARoy Loading…
2 tasks done
3.9.0
1
[DRAFT] Feature/ploidy support
#2091 opened Jan 12, 2026 by zhliUU • Draft
4 of 15 tasks
update cnvkit to reflect bug fixes blocked
#2051 opened Nov 11, 2025 by bounlu Contributor Loading…
3
Add mutect2 force calling using '--alleles' flag
#1952 opened Aug 11, 2025 by jchchiu Loading…
8 of 11 tasks
16
Make lane Column Optional in Samplesheet
#1943 opened Jul 21, 2025 by animesh Loading…
5
build: Set process arch for arm64
#1888 opened May 6, 2025 by edmundmiller Contributor • Draft
@edmundmiller
2
Collect intervallist channel output and propagate to genotyping step
#1872 opened Apr 24, 2025 by percyfal Loading…
11 tasks
6
POC: Usage for nf-core/references in nf-core/sarek
#1783 opened Jan 27, 2025 by maxulysse Member Loading…
11 tasks
1
Add files via upload - Posters using Sarek
#1773 opened Jan 15, 2025 by mateusfalco Loading…
11 tasks
1
feat: Add linting of FASTQ with FQ/LINT
#1763 opened Dec 17, 2024 by adamrtalbot Contributor Loading…
11 tasks
3.9.0
6
Use original QC values for Deepvariant after BQSR
#1733 opened Nov 15, 2024 by FriederikeHanssen Contributor • Draft
11 tasks
1
4
ProTip! What’s not been updated in a month: updated:<2026-08-22.