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Pull requests: nf-core/modules

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Pull requests list

Updated fqtk to version 0.4.0 Ready for Review
#12900 opened Sep 7, 2026 by Schmytzi Contributor Loading…
3 of 17 tasks
1
orthofinder: remove mv line
#12899 opened Sep 7, 2026 by FernandoDuarteF Contributor Loading…
3 of 17 tasks
8
CI: test composite change detection action
#12898 opened Sep 7, 2026 by adamrtalbot Contributor • Draft
3 of 7 tasks
fix(orftable_fasta_gtf_buildorfcatalogue): keep meta.id as the true sample id
#12896 opened Sep 6, 2026 by pinin4fjords Member Loading…
fix(fastq_qc_trim_filter_setstrandedness): expose fastp's merged reads Ready for Review
#12895 opened Sep 6, 2026 by pinin4fjords Member Loading…
fix(clustalo/align): wait for compression and propagate pigz failures
#12894 opened Sep 6, 2026 by dnncha Loading…
Update fastaguard to 1.0.0
#12892 opened Sep 5, 2026 by ehsanestaji Contributor • Draft
6 of 7 tasks
Add easypqp/library module
#12891 opened Sep 4, 2026 by jonasscheid Contributor Loading…
6 of 8 tasks
fix: deduplicate bclconvert FASTQ outputs
#12883 opened Sep 3, 2026 by atrigila Contributor • Draft
Fix miniconda version
#12879 opened Sep 3, 2026 by LouisLeNezet Contributor Loading…
17 tasks
3
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
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
ProTip! What’s not been updated in a month: updated:<2026-08-07.