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Pull requests: nf-core/modules

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166 Open 7,178 Closed
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Pull requests list

Add snpsift/annmem
#9892 opened Feb 4, 2026 by FriederikeHanssen Loading…
17 tasks
1
Apply strict syntax to VCFtools
#9890 opened Feb 4, 2026 by yz533cb Loading…
2 tasks done
Migrate upd, vcf2cytosure, vcfanno, and VerifyBamID2 to use topic channels Ready for Review
#9885 opened Feb 4, 2026 by ramprasadn Loading…
17 tasks
1
Update bcl_demultiplex size/m
#9883 opened Feb 4, 2026 by matthdsm Loading…
17 tasks
Add rgi/bwt
#9873 opened Feb 3, 2026 by vinisalazar Loading…
17 tasks done
1
Add fastqscreen aligner option
#9854 opened Feb 3, 2026 by pmoris Loading…
5 of 17 tasks
1
tabix is not needed, tbi computation is done by vep
#9821 opened Feb 2, 2026 by FriederikeHanssen Loading…
17 tasks
Fix meta_fb never defined in CELLRANGER_MULTI (#9798)
#9803 opened Jan 29, 2026 by SZhengP • Draft
4 of 17 tasks
1
5
update module: PERBASE
#9795 opened Jan 28, 2026 by camlloyd Loading…
3 of 17 tasks
1
4
Update CELLPOSE module to version 4.0.7 and adjust test configurations
#9793 opened Jan 28, 2026 by FloWuenne Loading…
6
Fix file extension for module PBMARKDUP
#9784 opened Jan 27, 2026 by sainsachiko Loading…
3 of 17 tasks
6
Swap bwa/mem to topic and combine output channels
#9783 opened Jan 27, 2026 by SPPearce Loading…
1
Add module stainwarpy/transformsegmask Ready for Review
#9778 opened Jan 26, 2026 by tckumarasekara Loading…
12 of 17 tasks
1
Add new module stainwarpy/register Ready for Review
#9777 opened Jan 26, 2026 by tckumarasekara Loading…
12 of 17 tasks
1
Add new module stainwarpy/extractchannel Ready for Review
#9776 opened Jan 26, 2026 by tckumarasekara Loading…
12 of 17 tasks
1
9
Add nextflow lint
#9726 opened Jan 21, 2026 by maxulysse Loading…
17 tasks
4
feat(yallhap/classify): Add new module for Y-chromosome haplogroup classification
#9704 opened Jan 20, 2026 by trianglegrrl • Draft
4 tasks done
5
Seqkit replace - fix #9647 and #9646
#9686 opened Jan 19, 2026 by ammaraziz Loading…
1
1
Update all deeptools conda environment YAML files to version 3.5.6
#9685 opened Jan 16, 2026 by bentyeh Loading…
2 of 17 tasks
7
Add ViralConsensus module
#9655 opened Jan 14, 2026 by lucaspatel Loading…
15 of 17 tasks
1
15
add nirvana
#9633 opened Jan 9, 2026 by FriederikeHanssen Loading…
17 tasks
8
BBsplit unmapped - enhancement
#9627 opened Jan 8, 2026 by EladH1 Loading…
4 of 17 tasks
3
Add gapseq modules for bacterial metabolic pathway analysis
#9620 opened Jan 7, 2026 by Copilot AI • Draft
1
@brovolia
traitar module is drafted size/l
#9605 opened Dec 22, 2025 by brovolia Loading…
1
@brovolia
36
Fix fastANI module
#9583 opened Dec 17, 2025 by Ethan-Hetrick Loading…
10 of 17 tasks
36
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