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Pull requests: nf-core/sarek

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Pull requests list

FIX: Update plugin dependencies
#2170 opened Apr 13, 2026 by maxulysse Member Loading…
11 tasks
4
Prepare RC 3.8.2
#2169 opened Apr 13, 2026 by maxulysse Member Loading…
11 tasks
2
Release 3.8.2
#2168 opened Apr 13, 2026 by famosab Contributor Loading…
11 tasks
2
Add xengsort contamination removal support
#2161 opened Mar 25, 2026 by famosab Contributor Loading…
11 tasks done
@xinghansun
2
Fix --save_output_as_bam flag
#2154 opened Mar 9, 2026 by FriederikeHanssen Contributor Loading…
5 tasks
10
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
Output syntax Migration
#2066 opened Dec 3, 2025 by edmundmiller Contributor • Draft
11 tasks
@edmundmiller
5
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
Support for PureCN
#1710 opened Oct 29, 2024 by lbeltrame • Draft
3 of 14 tasks
@lbeltrame
17
Add full test report
#1701 opened Oct 28, 2024 by edmundmiller Contributor • Draft
11 tasks
1
@maxulysse @edmundmiller
2
[DRAFT] Add telseq "a software that estimates telomere length "
#1665 opened Sep 26, 2024 by lindenb Contributor Loading…
6 of 11 tasks
Add deepsomatic tool
#1647 opened Sep 10, 2024 by vaxyzek Loading…
11 tasks
8
Asmultipcf implementation for multi-sample ASCAT CNV calling
#1646 opened Sep 4, 2024 by alexanderchang1 Contributor Loading…
8 tasks done
2
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