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Pull requests: nf-core/sarek

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Pull requests list

WIP: Fix warning nf corelint
#1955 opened Aug 14, 2025 by maxulysse Loading…
11 tasks
3
Change freebayes tests from gzip to md5sum, update freebayes and add QUAL filtering
#1953 opened Aug 12, 2025 by famosab Loading…
1 of 11 tasks
13
Add mutect2 force calling using '--alleles' flag
#1952 opened Aug 11, 2025 by jchchiu • Draft
1 task done
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
Varlociraptor integration
#1940 opened Jul 15, 2025 by famosab Loading…
6 of 11 tasks
3.6
38
[DRAFT] Changes to UMI processing
#1937 opened Jul 9, 2025 by SPPearce • Draft
6
Refactor to adhere to language server
#1912 opened May 30, 2025 by FriederikeHanssen • Draft
11 tasks
3.6
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
Udate GATK modules - Fix output line lack of specificity
#1839 opened Mar 18, 2025 by johnoooh Loading…
7 of 11 tasks
9
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
5
Use original QC values for Deepvariant after BQSR
#1733 opened Nov 15, 2024 by FriederikeHanssen • Draft
11 tasks
3
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
14
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
Try to simplify params.tools usage
#1667 opened Sep 30, 2024 by maxulysse Loading…
11 tasks
1
[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
ProTip! Updated in the last three days: updated:>2025-08-16.