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Pull requests: nf-core/sarek

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Pull requests list

Important! Template update for nf-core/tools v3.3.1
#1913 opened Jun 2, 2025 by nf-core-bot Loading…
@mashehu @mirpedrol
7
Refactor to adhere to language server
#1912 opened May 30, 2025 by FriederikeHanssen • Draft
11 tasks
1
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
Add checks for uniqueness of sample ids
#1902 opened May 26, 2025 by famosab Loading…
1 of 11 tasks
3.6
1
5
Add information on gatk_spark and save_output_as_bam
#1896 opened May 21, 2025 by famosab Loading…
2 of 11 tasks
3.6
1
2
docs: Cleanup subway map
#1890 opened May 12, 2025 by edmundmiller Loading… 3.6
@edmundmiller
9
build: Set process arch for arm64
#1888 opened May 6, 2025 by edmundmiller • Draft
@edmundmiller
2
Update contributor list
#1885 opened May 5, 2025 by maxulysse Loading…
11 tasks
3.6
3
Collect intervallist channel output and propagate to genotyping step
#1872 opened Apr 24, 2025 by percyfal Loading…
11 tasks
3
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
Modification from NF Language server
#1779 opened Jan 23, 2025 by maxulysse Loading…
11 tasks
3.6
5
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
add_dysgu_sarek
#1590 opened Jul 11, 2024 by poddarharsh15 Loading…
11 tasks
14
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