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Pull requests: nf-core/modules

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140 Open 4,625 Closed
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Pull requests list

Add extra input channel to KRAKEN2/ADD
#7721 opened Feb 28, 2025 by jfy133 • Draft
17 tasks
2
Fix fastq_create_umi_consensus_fgbio and swap to nf-test
#7718 opened Feb 28, 2025 by SPPearce • Review required
1
3
[DO NOT MERGE] Test gpu runners
#7521 opened Feb 27, 2025 by mashehu • Draft
bioformats2raw module
#7518 opened Feb 26, 2025 by CaroAMN • Review required
8 of 9 tasks
1
compressing output files
#7507 opened Feb 20, 2025 by DimitriTernovoj • Review required
1
new module: FASTQDL
#7506 opened Feb 20, 2025 by camlloyd • Review required
11 of 17 tasks
1
Update version modules tcoffee to 13.46.1
#7498 opened Feb 19, 2025 by luisas • Review required
17 tasks
gatk4/markduplicates - pipe uncompressed output to speed up CRAM writing
#7497 opened Feb 18, 2025 by pontushojer • Draft
11 of 17 tasks
Krona module updates
#7489 opened Feb 16, 2025 by dialvarezs • Review required
2 of 17 tasks
Add index format to samtools view Ready for Review
#7481 opened Feb 14, 2025 by fellen31 • Review required
17 tasks
7
simplify assertion for stable files in a folder
#7462 opened Feb 10, 2025 by maxulysse • Draft
17 tasks
6
update prettier to 3.5.0
#7459 opened Feb 10, 2025 by mashehu • Approved
Rattle cluster
#7447 opened Feb 6, 2025 by chriswyatt1 • Review required
2
Update KRAKEN2/ADD to allow proper resuming
#7445 opened Feb 6, 2025 by jfy133 • Approved
17 tasks
New samtools/bgzip module to produce BGZF-compressed files.
#7433 opened Feb 5, 2025 by charles-plessy • Draft
17 tasks done
2
[DO NOT MERGE] Test PR to see how the template would look like when creating a new modules WIP Work in progress
#7430 opened Feb 4, 2025 by mirpedrol • Draft
8
Move output format information to the first queue channel of last/mafconvert
#7428 opened Feb 4, 2025 by charles-plessy • Approved
17 tasks done
Update biocontainers/cooler Docker tag to v0.10.3
#7419 opened Feb 1, 2025 by renovate bot • Review required
2 tasks
Update biocontainers/cnvkit Docker tag to v0.9.12
#7418 opened Feb 1, 2025 by renovate bot • Review required
2 tasks
add another clean-up step to GHA
#7416 opened Jan 31, 2025 by mirpedrol • Review required
1
Add db to output meta object for diamond/blastp
#7403 opened Jan 30, 2025 by erikrikarddaniel • Review required
2 of 17 tasks
5
Hifiadapterfilt
#7398 opened Jan 30, 2025 by Ge94 • Changes requested
14 of 17 tasks
1
8
Fix falco sample names
#7394 opened Jan 30, 2025 by MartinGrignard • Review required
5
should emit either tbi or csi
#7386 opened Jan 28, 2025 by tkchafin • Approved
17 tasks
3
index should be emitted as either tbi or csi
#7385 opened Jan 28, 2025 by tkchafin • Review required
17 tasks
1
ProTip! Exclude everything labeled bug with -label:bug.