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Pull requests: nf-core/modules

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Pull requests list

Add BEAGLE5 imputation subworkflow
#9550 opened Dec 10, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
Version update: Modkit repair, callmods and bedmethyltobigwig
#9547 opened Dec 10, 2025 by jkh00 Loading…
2 of 17 tasks
2
Rseqc add bam index - topics-based versions - version bump bug Something isn't working
#9546 opened Dec 10, 2025 by rhassaine Loading…
13 of 17 tasks
1
@rhassaine
Update BWA_INDEX memory formula to match BWAMEM2_INDEX pattern
#9528 opened Dec 8, 2025 by Copilot AI • Draft
11 of 17 tasks
1
@edmundmiller
Update GLIMPSE sbwf Ready for Review update subworkflow
#9524 opened Dec 8, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests
#9521 opened Dec 8, 2025 by kornkv Loading…
bump vcf2maf to ensembl-vep=113.4 and update containers
#9515 opened Dec 6, 2025 by JustinBellavance Loading…
17 tasks
2
Assemblyscan 1.0.0
#9506 opened Dec 4, 2025 by eit-maxlcummins Loading…
10 tasks done
Get conda envs
#9504 opened Dec 4, 2025 by mirpedrol Loading…
update bclconvert with topic
#9494 opened Dec 2, 2025 by matthdsm Loading…
17 tasks
1
RiboCode - prepare_transcripts, metaplots, ribocode
#9485 opened Dec 1, 2025 by JackCurragh Loading…
11 of 17 tasks
1
13
Hiphase: bump to version 1.5.0; use wave container; emit phased bam file enhancement New feature or request Ready for Review update module
#9477 opened Nov 28, 2025 by chaochaowong Loading…
12 of 14 tasks
@chaochaowong
fix issue 9424: MultiQC report handling for AWS batch with S3 workDir
#9455 opened Nov 25, 2025 by SZhengP Loading…
3 of 17 tasks
1
Add minimac4 imputation subworkfllow new subworkflow
#9451 opened Nov 25, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
Add quilt imputation subworkflow new subworkflow
#9443 opened Nov 24, 2025 by LouisLeNezet Loading…
8 of 17 tasks
@LouisLeNezet
fix: kmer env output missing when scientific notation found
#9442 opened Nov 24, 2025 by CormacKinsella Loading…
17 tasks
1
Update output paths in bases2fastq module
#9436 opened Nov 21, 2025 by lucacozzuto Loading…
6 of 16 tasks
Refactor GAWK implicit closures
#9435 opened Nov 21, 2025 by DLBPointon Loading…
Update glimpse2 imputation subworkflow Ready for Review subworkflows update module update subworkflow
#9434 opened Nov 20, 2025 by LouisLeNezet Loading…
8 of 17 tasks
@LouisLeNezet
5
Updare fgbio/copyumifromreadname
#9373 opened Nov 10, 2025 by SPPearce • Draft
Add module: TRIDENT_FETCH
#9360 opened Nov 7, 2025 by TCLamnidis Loading…
4 of 20 tasks
5
Vcf vembrane
#9345 opened Nov 5, 2025 by dhtt • Draft
12 of 17 tasks
@dhtt
1
Use tar --no-same-owner option for untar module
#9338 opened Nov 4, 2025 by nathanweeks Loading…
2 of 17 tasks
10
Add fq2bam fq align dd bwamem
#9309 opened Oct 30, 2025 by eduard-watchmaker Loading…
17 tasks
58
Restructuring how symlinks work to avoid conflicts with file permissions
#9308 opened Oct 30, 2025 by gburnett-nvidia Loading…
8 of 17 tasks
1
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