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Pull requests: nf-core/sarek

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Pull requests list

Addition of bbsplit for filtering of genomic contaminants
#1850 opened Mar 26, 2025 by apsteinberg • Draft
11 tasks
12
Fix bug in sample_lane_id in addReadgroupToMeta
#1849 opened Mar 25, 2025 by thiago-miller • Review required
11 tasks
5
1846 pixel distance md
#1848 opened Mar 25, 2025 by kjellinjonas • Review required
5 of 11 tasks
2
Udate GATK modules - Fix output line lack of specificity
#1839 opened Mar 18, 2025 by johnoooh • Changes requested
7 of 11 tasks
9
[WIP] Integrate parabricks
#1804 opened Feb 19, 2025 by famosab • Review required
11 tasks
9
POC: Usage for nf-core/references in nf-core/sarek
#1783 opened Jan 27, 2025 by maxulysse • Review required
11 tasks
1
Important! Template update for nf-core/tools v3.2.0
#1782 opened Jan 27, 2025 by nf-core-bot • Review required
4
Modification from NF Language server
#1779 opened Jan 23, 2025 by maxulysse • Review required
11 tasks
4
Add files via upload - Posters using Sarek
#1773 opened Jan 15, 2025 by mlfalco-bioinfo • Review required
11 tasks
1
Add bcftools normalization
#1770 opened Jan 13, 2025 by maxulysse • Review required
5 of 22 tasks
6
feat: Add linting of FASTQ with FQ/LINT
#1763 opened Dec 17, 2024 by adamrtalbot • Review required
11 tasks
5
Implemented TMB score calculation
#1738 opened Nov 20, 2024 by bounlu • Review required
1 of 11 tasks
7
Implemented MSISENSORPRO tumor-only analysis
#1737 opened Nov 20, 2024 by bounlu • Review required
1 of 11 tasks
13
Use original QC values for Deepvariant after BQSR
#1733 opened Nov 15, 2024 by FriederikeHanssen • Draft
11 tasks
3
ci: Remove pytest-workflow
#1729 opened Nov 8, 2024 by edmundmiller • Draft
@edmundmiller
1
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
5
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 • Review required
11 tasks
1
[DRAFT] Add telseq "a software that estimates telomere length "
#1665 opened Sep 26, 2024 by lindenb • Review required
6 of 11 tasks
Add deepsomatic tool
#1647 opened Sep 10, 2024 by vaxyzek • Review required
11 tasks
8
Asmultipcf implementation for multi-sample ASCAT CNV calling
#1646 opened Sep 4, 2024 by alexanderchang1 • Review required
8 tasks done
2
add_dysgu_sarek
#1590 opened Jul 11, 2024 by poddarharsh15 • Review required
11 tasks
14
vardictjava variant calling workflow
#1582 opened Jul 3, 2024 by eolaniru • Changes requested
11 tasks
13
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