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Pull requests: nf-core/modules

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Pull requests list

chore(deps): update dependency prettier to v3.8.1
#9813 opened Feb 1, 2026 by renovate bot Loading…
2 tasks
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14
#9812 opened Feb 1, 2026 by renovate bot Loading…
2 tasks
chore(deps): update dependency nextflow-io/nextflow to v25.10.3
#9811 opened Feb 1, 2026 by renovate bot Loading…
2 tasks
Samtools mpileup input update enhancement New feature or request
#9810 opened Jan 30, 2026 by Krannich479 Loading…
8 of 17 tasks
1
@Krannich479
1
Fix meta_fb never defined in CELLRANGER_MULTI (#9798)
#9803 opened Jan 29, 2026 by SZhengP • Draft
4 of 17 tasks
1
5
Add topic channels to Chromograph, DeepVariant, ExpansionHunter, and Stranger Ready for Review
#9800 opened Jan 29, 2026 by ramprasadn Loading…
17 tasks
5
Update module BFTOOLS/SHOWINF: Changed for compressed output
#9797 opened Jan 28, 2026 by AlexBarbera • Draft
1 task done
2
Convert untar, pigz/compress, kallisto/index, samtools/index, bowtie2/build to topic versions
#9796 opened Jan 28, 2026 by pinin4fjords Loading…
2 of 3 tasks
17
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
4
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
8
Update Rundbcan modules
#9768 opened Jan 26, 2026 by HaidYi Loading…
11 of 16 tasks
@Xinpeng021001
4
Fix variable redeclarations for strict syntax compliance (from branch)
#9756 opened Jan 22, 2026 by ewels Loading…
miniasm/ updated to use the new versions topics
#9755 opened Jan 22, 2026 by MohineTAlam Loading…
17 tasks done
8
migrate toulligqc to topic versions
#9750 opened Jan 22, 2026 by eit-maxlcummins Loading…
5 of 10 tasks
7
migrate untar to versions topic
#9749 opened Jan 22, 2026 by eit-maxlcummins Loading…
5 of 10 tasks
1
update to new versions capture for checkm2 databasedownload and checkm2 predict
#9744 opened Jan 22, 2026 by eit-maxlcummins Loading…
5 of 10 tasks
10
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
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