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Pull requests: nf-core/sarek

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Pull requests list

avoid misleading sample-sheet errors on unrelated pipeline abort (#1629)
#2245 opened Jul 22, 2026 by asp8200 Contributor Loading…
1
chore(modules): migrate local modules to versions topic channel
#2244 opened Jul 21, 2026 by FriederikeHanssen Contributor Loading…
chore(modules): migrate cnvkit modules to versions topic channel
#2243 opened Jul 21, 2026 by FriederikeHanssen Contributor Loading…
chore(modules): migrate QC/coverage modules to versions topic channel
#2242 opened Jul 21, 2026 by FriederikeHanssen Contributor Loading…
chore(modules): migrate samtools modules to versions topic channel
#2241 opened Jul 21, 2026 by FriederikeHanssen Contributor Loading…
1
Refactor BQSR: route SV/CNV callers to markdup output (pre-BQSR)
#2205 opened Jun 9, 2026 by FriederikeHanssen Contributor • Draft
3 tasks
1
Remove executor dependency from accelerator directive
#2181 opened May 7, 2026 by pditommaso Loading…
3 tasks
5
Add GPU-accelerated mutectcaller from Parabricks
#2180 opened May 6, 2026 by gburnett-nvidia Loading…
3
Add Parabricks (GPU-based) DeepVariant
#2177 opened Apr 29, 2026 by gburnett-nvidia Loading…
9 tasks done
3
Add Parabricks (GPU-based) Haplotypecaller
#2176 opened Apr 28, 2026 by gburnett-nvidia Loading…
9 tasks done
36
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
Investigating potential mutect2 filter bug
#2062 opened Nov 27, 2025 by maxulysse Member Loading…
11 tasks
2
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
WIP Internal Benchmarking
#1721 opened Nov 1, 2024 by famosab Contributor • Draft
11 tasks
7
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