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Pull requests: nf-core/modules

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Pull requests list

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 xenium ranger modules and subworkflows
#9525 opened Dec 8, 2025 by an-altosian Loading…
11 of 17 tasks
12
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 • Draft
fix(tximport): handle tx2gene files with extra columns
#9520 opened Dec 8, 2025 by pinin4fjords Loading…
3 tasks done
1
4
bump vcf2maf to ensembl-vep=113.4 and update containers
#9515 opened Dec 6, 2025 by JustinBellavance Loading…
17 tasks
2
Bump TRGT to 4.1.0
#9514 opened Dec 6, 2025 by fellen31 Loading…
17 tasks
Add strdrop/call
#9513 opened Dec 6, 2025 by fellen31 • Draft
17 tasks
Fix dream to show more than 10 results
#9507 opened Dec 4, 2025 by delfiterradas • Draft
17 tasks
1
1
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…
Add module picard/collectvariantcallingmetrics new module Adding a new module Ready for Review
#9502 opened Dec 4, 2025 by georgiakes Loading…
11 of 16 tasks
1
6
update bclconvert with topic
#9494 opened Dec 2, 2025 by matthdsm Loading…
17 tasks
1
5787 new module whatshap/stats
#9490 opened Dec 2, 2025 by eliottBo Loading…
8 of 17 tasks
1
@eliottBo
12
RiboCode - prepare_transcripts, metaplots, ribocode
#9485 opened Dec 1, 2025 by JackCurragh Loading…
11 of 17 tasks
1
13
plastid metagene_generate, make_wiggle, psite
#9482 opened Dec 1, 2025 by suhrig Loading…
12 of 14 tasks
23
Hiphase: bump to version 1.5.0; use wave container; add phased bam file as an output enhancement New feature or request Ready for Review update module
#9477 opened Nov 28, 2025 by chaochaowong Loading…
12 of 14 tasks
@chaochaowong
New Module - Orfipy new module Adding a new module Ready for Review ready to merge
#9476 opened Nov 28, 2025 by khersameesh24 Loading…
1
@khersameesh24
4
New module - TD2 (added modules for td2.longorfs & td2.predict) new module Adding a new module Ready for Review ready to merge
#9475 opened Nov 28, 2025 by khersameesh24 Loading…
1
@khersameesh24
30
Fix test path modification
#9465 opened Nov 26, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
1
Update shapeit test and input tuple Ready for Review update subworkflow
#9463 opened Nov 26, 2025 by LouisLeNezet Loading…
13 of 17 tasks
@LouisLeNezet
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
ProTip! Exclude everything labeled bug with -label:bug.