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Pull requests: nf-core/modules

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Pull requests list

fix: deduplicate bclconvert FASTQ outputs
#12883 opened Sep 3, 2026 by atrigila Contributor • Draft
fix: align meta.yml input/output with main.nf across all modules and subworkflows size/xl
#12882 opened Sep 3, 2026 by bentsherman • Draft
8 of 11 tasks
1
New module for delly. Using version 2.x.x with sr instead of call
#12880 opened Sep 3, 2026 by gustav-001 Contributor Loading…
1 of 3 tasks
3
Fix miniconda version
#12879 opened Sep 3, 2026 by LouisLeNezet Contributor Loading…
17 tasks
3
update containers from selfhosted registry to seqera containers
#12878 opened Sep 3, 2026 by CaroAMN Contributor Loading…
17 tasks
1
feat(vamb/bin): add GPU support
#12876 opened Sep 3, 2026 by dialvarezs Member Loading…
10 tasks done
Bump TMB Ready for Review
#12867 opened Sep 2, 2026 by georgiakes Member Loading…
1 of 17 tasks
Bump t1k Ready for Review
#12866 opened Sep 2, 2026 by georgiakes Member Loading…
1 of 17 tasks
New module: xengsort/classify Ready for Review
#12864 opened Sep 1, 2026 by LeonHornich Contributor Loading…
12 of 14 tasks
Update pre-commit hooks size/xs
#12860 opened Sep 1, 2026 by renovate Bot Loading…
2 tasks
samtools/merge: emit .bai/.crai index files by default (fixes #4261)
#12859 opened Sep 1, 2026 by ramakrishna-p21 Loading…
12 tasks done
1
6
update module: bioformats2raw
#12857 opened Aug 31, 2026 by camlloyd Member Loading…
2 of 17 tasks
1
Remove cplex from optitype module due to licensing issues
#12848 opened Aug 31, 2026 by SpikyClip Contributor Loading…
Add STAR Suite alignment and genome generation modules
#12826 opened Aug 27, 2026 by lhhunghimself Loading…
11 of 12 tasks
1
12801 bug in gsea module related with multiple gene sets processing size/m
#12821 opened Aug 26, 2026 by brovolia Contributor Loading…
1
15
Add parabricks/deepsomatic size/m
#12797 opened Aug 26, 2026 by SPPearce Contributor • Draft
3
Migrate starfusion/build to topics size/l
#12748 opened Aug 18, 2026 by mribeirodantas Member Loading…
17 tasks
1
@mribeirodantas
16
Remove fixed UMI-tools seeds Do not merge yet
#12662 opened Aug 12, 2026 by pinin4fjords Member Loading…
5
Add STRAGLR module
#12644 opened Aug 10, 2026 by lukejroche Loading…
2 tasks
1
1
Update to topic qualimap
#12625 opened Aug 7, 2026 by LouisLeNezet Contributor Loading…
17 tasks
1
@LouisLeNezet
7
Provide .fna support for pbmm2/align
#12602 opened Aug 6, 2026 by stvdsomp Loading…
6 tasks done
4
fix probe-set inclusion assertion size/m
#12601 opened Aug 6, 2026 by fmalmeida Contributor Loading…
1
@fmalmeida
6
Update to topic phyloflash Do not merge yet
#12577 opened Aug 4, 2026 by LouisLeNezet Contributor Loading…
17 tasks
1
@LouisLeNezet
5
Add subworkflow for gridss somatic structural variant calling
#12574 opened Aug 4, 2026 by imsarath Contributor Loading…
14 of 17 tasks
1
@imsarath
12
Swap repeatmodeler to topics conda-fail size/m
#12513 opened Aug 3, 2026 by SPPearce Contributor • Draft
17 tasks
2
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