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Pull requests: nf-core/modules

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Pull requests list

Hiphase: update version to 1.5.0 and add phased bam file as an output enhancement New feature or request update module
#9477 opened Nov 28, 2025 by chaochaowong Loading…
12 of 14 tasks
@chaochaowong
New Module - Orfipy
#9476 opened Nov 28, 2025 by khersameesh24 Loading…
1
New module - TD2 (added modules for td2.longorfs & td2.predict)
#9475 opened Nov 28, 2025 by khersameesh24 Loading…
1
feat(fastq_qc_trim_filter_setstrandedness): Add Bowtie2 as alternative rRNA removal tool
#9474 opened Nov 28, 2025 by pinin4fjords • Draft
4 tasks done
2
Enable complex contrast strings in DESeq2
#9473 opened Nov 27, 2025 by delfiterradas Loading…
2 of 17 tasks
1
@delfiterradas
3
Declare deepvariant optional html output
#9469 opened Nov 27, 2025 by peterpru Loading…
8 of 17 tasks
@peterpru
2
Update test files for Glimpse Ready for Review
#9467 opened Nov 26, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
6
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
#9463 opened Nov 26, 2025 by LouisLeNezet Loading…
17 tasks
@LouisLeNezet
Add module PBMARKDUP
#9457 opened Nov 25, 2025 by sainsachiko Loading…
14 of 17 tasks
5
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
update and add topics to snakemake module
#9454 opened Nov 25, 2025 by maxulysse Loading…
17 tasks
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…
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…
17 tasks
@LouisLeNezet
New module: whatshap/phase
#9431 opened Nov 19, 2025 by HaidYi Loading…
12 of 17 tasks
1
@HaidYi
16
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
8
Add fq2bam fq align dd bwamem
#9309 opened Oct 30, 2025 by eduard-watchmaker Loading…
17 tasks
54
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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