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Pull requests: nf-core/modules

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Pull requests list

Remove fai index from bowtie2 modules
#11537 opened May 5, 2026 by Kevin-Brockers Contributor Loading…
5 of 6 tasks
Update input channel chromap modules
#11536 opened May 5, 2026 by Kevin-Brockers Contributor Loading…
9 tasks done
Update to topics fusionreport/*
#11535 opened May 5, 2026 by LouisLeNezet Contributor Loading…
17 tasks
2
@LouisLeNezet
nanofilt topic channel migration
#11534 opened May 5, 2026 by FernandoDuarteF Contributor Loading…
17 tasks
1
Update to topics fusioninspector
#11533 opened May 5, 2026 by LouisLeNezet Contributor Loading…
17 tasks
1
@LouisLeNezet
Fix dumpParametersToJson to be compatible with parameter typing
#11532 opened May 5, 2026 by nvnieuwk Contributor Loading…
9
Bump VSEARCH version to 2.31.0
#11530 opened May 5, 2026 by pieterprovoost Loading…
2 of 17 tasks
fix(tximeta/tximport, quant_tximport_summarizedexperiment, quantify_pseudo_alignment): publish augmented tx2gene actually used by tximport
#11526 opened May 5, 2026 by pinin4fjords Member Loading…
4 of 5 tasks
Update to topics fcs
#11522 opened May 4, 2026 by LouisLeNezet Contributor Loading…
17 tasks
1
@LouisLeNezet
fix: pass the expected input to bwamem1_index and bwamem2_index
#11520 opened May 4, 2026 by piplus2 Loading…
10 of 16 tasks
1
2
New module: sdrfpipelines/convertmhcquant
#11514 opened May 4, 2026 by jonasscheid Contributor Loading…
12 of 14 tasks
10
Add module to fetch SDRF files from PRIDE Archive
#11513 opened May 4, 2026 by jonasscheid Contributor Loading…
14 tasks done
5
feat(spikeinterface/sort): add module wrapping SpikeInterface 0.101.2 spike sorting
#11464 opened May 3, 2026 by olaflaitinen Member • Draft
8 of 12 tasks
Update gamma/gamma to using the versions topic channel size/s
#11462 opened May 1, 2026 by mribeirodantas Member Loading…
14 of 17 tasks
1
@mribeirodantas
1
nf-core-module-dev bots updating hmmer tools: hmmbuild, hmmsearch, hmmalign to topic versions and latest standards size/l
#11458 opened May 1, 2026 by vagkaratzas Contributor Loading…
9 of 17 tasks
1
feat: allow bwa-mem to output sam format
#11457 opened May 1, 2026 by piplus2 Loading…
7 of 17 tasks
1
2
Update whamg: topic versions, stub block, sanitizeOutput
#11450 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
3
Update wfmash: topic versions, stub block, sanitizeOutput
#11449 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
1
Update smoothxg: topic versions, stub block, sanitizeOutput
#11448 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
4
Update seqsero2: topic versions, stub block, sanitizeOutput
#11446 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
1
Update salsa2: topic versions, stub block, sanitizeOutput
#11445 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
2
Update mygene: topic versions, stub block, sanitizeOutput
#11441 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
3
Update fasttree: topic versions, stub block, sanitizeOutput
#11439 opened Apr 30, 2026 by HReed1 Contributor Loading…
5 tasks done
1
Add stub block and migrate plasmidid to topic channels
#11438 opened Apr 30, 2026 by HReed1 Contributor Loading…
7
Add stub block and migrate pairix to topic channels
#11437 opened Apr 30, 2026 by HReed1 Contributor Loading…
2
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