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Pull requests: nf-core/sarek

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Pull requests list

Add developer guidelines and CLAUDE.md
#2144 opened Feb 20, 2026 by FriederikeHanssen Loading…
2 tasks
4
Replace custom Slack notifications with nf-slack plugin
#2142 opened Feb 13, 2026 by FriederikeHanssen • Draft
3 tasks
4
Revise ASCAT resource generation instructions
#2135 opened Feb 10, 2026 by CharlesARoy Loading…
2 tasks done
3.9.0
1
Fix alignment related strict syntax and lane issue Ready for Review
#2117 opened Jan 30, 2026 by famosab Loading…
11 tasks
3.9.0
1
10
[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 • Draft
11 tasks
@edmundmiller
5
Investigating potential mutect2 filter bug
#2062 opened Nov 27, 2025 by maxulysse Loading…
11 tasks
2
update cnvkit to reflect bug fixes blocked
#2051 opened Nov 11, 2025 by bounlu 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 • 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 Loading…
11 tasks
1
Add files via upload - Posters using Sarek
#1773 opened Jan 15, 2025 by mlfalco-bioinfo Loading…
11 tasks
1
feat: Add linting of FASTQ with FQ/LINT
#1763 opened Dec 17, 2024 by adamrtalbot Loading…
11 tasks
3.9.0
6
Use original QC values for Deepvariant after BQSR
#1733 opened Nov 15, 2024 by FriederikeHanssen • Draft
11 tasks
1
4
WIP Internal Benchmarking
#1721 opened Nov 1, 2024 by famosab • 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 • Draft
11 tasks
1
@maxulysse @edmundmiller
2
[DRAFT] Add telseq "a software that estimates telomere length "
#1665 opened Sep 26, 2024 by lindenb 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 Loading…
8 tasks done
2
add_dysgu_sarek
#1590 opened Jul 11, 2024 by poddarharsh15 Loading…
11 tasks
14
vardictjava variant calling workflow
#1582 opened Jul 3, 2024 by eolaniru Loading…
11 tasks
14
Split variantannotation in its own pipeline and import it
#1561 opened Jun 11, 2024 by maxulysse • Draft
11 tasks
7
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