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Pull requests: nf-core/sarek

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Pull requests list

Adjust VEP versions in snap files that were forgotten when updating
#1998 opened Sep 27, 2025 by famosab Loading…
1 of 11 tasks
3
Adress review comments
#1989 opened Sep 18, 2025 by FriederikeHanssen • Draft
11 tasks
Nft utils tuple match warn
#1986 opened Sep 17, 2025 by maxulysse • Draft
11 tasks
1
Draft PR to apply feeedback to BBSplit
#1983 opened Sep 16, 2025 by FriederikeHanssen • Draft
11 tasks
1
Prepare genome refactor
#1979 opened Sep 10, 2025 by maxulysse Loading…
11 tasks
@maxulysse
1
Update bcftools/annotate to pick up columns file input
#1973 opened Sep 9, 2025 by heuermh Loading…
11 tasks
2
Release 3.6.0
#1968 opened Sep 8, 2025 by maxulysse • Draft
11 tasks
3
WIP: Fix warning nf core lint and nextflow lint
#1955 opened Aug 14, 2025 by maxulysse Loading…
11 tasks
28
Add mutect2 force calling using '--alleles' flag
#1952 opened Aug 11, 2025 by jchchiu Loading…
8 of 11 tasks
13
Parallel CRAM creation during GATK MarkDuplicates
#1947 opened Aug 4, 2025 by tsnowlan Loading…
2 of 5 tasks
Make lane Column Optional in Samplesheet
#1943 opened Jul 21, 2025 by animesh Loading…
5
Add varlociraptor as variant postprocessing tool
#1940 opened Jul 15, 2025 by famosab Loading…
6 of 12 tasks
3.7
74
Refactor to adhere to language server
#1912 opened May 30, 2025 by FriederikeHanssen • Draft
11 tasks
5
Update ApplyBQSR module to output cram on bam input to fix restart from recalibration
#1911 opened May 30, 2025 by FriederikeHanssen • Draft
11 tasks
1
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
Addition of bbsplit for filtering of genomic contaminants
#1850 opened Mar 26, 2025 by apsteinberg Loading…
11 tasks
39
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
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
15
Add full test report
#1701 opened Oct 28, 2024 by edmundmiller • Draft
11 tasks
1
@maxulysse @edmundmiller
2
FEAT: Auto CHANGELOG GHA
#1688 opened Oct 14, 2024 by maxulysse • Draft
2
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