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Pull requests: nf-core/modules

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Pull requests list

strict syntax + versions topic
#9693 opened Jan 19, 2026 by vagkaratzas Loading…
6 of 17 tasks
Update CHECKM2_PREDICT to allow more flexible pickup of database file
#9691 opened Jan 19, 2026 by jfy133 Loading…
17 tasks
1
parabricks topic port
#9690 opened Jan 19, 2026 by famosab Loading…
17 tasks
1
fix: Nextflow 25 strict syntax compliance for modules and subworkflows
#9688 opened Jan 19, 2026 by pinin4fjords • Draft
1 of 3 tasks
Seqkit replace - fix #9647 and #9646
#9686 opened Jan 19, 2026 by ammaraziz Loading…
1
1
Update all deeptools conda environment YAML files to version 3.5.6
#9685 opened Jan 16, 2026 by bentyeh Loading…
2 of 17 tasks
2
Fix variable redeclarations for strict syntax compliance
#9684 opened Jan 16, 2026 by ewels • Draft
20
Fix deprecation message declarations for strict syntax compliance
#9682 opened Jan 16, 2026 by ewels Loading…
1
Fix environment variable references for strict syntax compliance WIP Work in progress
#9681 opened Jan 16, 2026 by ewels • Draft
4
Fix --help with strict syntax mode
#9680 opened Jan 16, 2026 by ewels Loading…
3
version topics, strict syntax, stub tests
#9679 opened Jan 16, 2026 by vagkaratzas Loading…
7 of 17 tasks
11
Samtools quickcheck
#9678 opened Jan 16, 2026 by Krannich479 Loading…
9 of 17 tasks
1
@Krannich479
snpeff and vep - topics for reports
#9677 opened Jan 16, 2026 by maxulysse Loading…
17 tasks
5
fix(picard/markduplicates): add missing bai index file to stub output
#9676 opened Jan 16, 2026 by adamrtalbot Loading…
Fix abundance_differential_filter to only generate one normalized matrix with dream
#9675 opened Jan 15, 2026 by delfiterradas Loading…
17 tasks
1
@delfiterradas
6
Update amulety modules
#9674 opened Jan 15, 2026 by ggabernet Loading…
8
feat(merquryfk/merquryfk): use topic versions and emit all images in single channel Do not merge yet
#9672 opened Jan 15, 2026 by prototaxites • Draft
3 of 17 tasks
7
feat: hisat3n/build module Ready for Review
#9668 opened Jan 15, 2026 by emmcauley Loading…
12 of 17 tasks
1
fix(fastk/merge): use topic versions and update snapshots Ready for Review
#9666 opened Jan 15, 2026 by prototaxites Loading…
3 of 17 tasks
5
new subworkflow - fastq shortreads preprocess qc
#9665 opened Jan 15, 2026 by vagkaratzas Loading…
8 of 17 tasks
1
Add tmb module new module Adding a new module Ready for Review
#9660 opened Jan 15, 2026 by georgiakes Loading…
11 of 17 tasks
11
Shigapass
#9658 opened Jan 15, 2026 by eit-maxlcummins Loading…
12 of 17 tasks
1
Prepare gens input data module
#9656 opened Jan 15, 2026 by Jakob37 • Draft
1 of 17 tasks
1
Add ViralConsensus module
#9655 opened Jan 14, 2026 by lucaspatel Loading…
15 of 17 tasks
1
Emit both png and pdf plots in deseq2
#9654 opened Jan 14, 2026 by delfiterradas Loading…
17 tasks
1
@delfiterradas
1
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