8000 Issues · nf-core/viralrecon · GitHub
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28 Open 156 Closed
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Issues list

Use snpeff nf-core modules instead of local modules
#475 opened Mar 21, 2025 by saramonzon
2
@Aberdur
Use kraken add fasta build subworkflow instead of local kraken2 build module
#474 opened Mar 21, 2025 by saramonzon
Update local modules with nf-test logic
#473 opened Mar 21, 2025 by saramonzon
@saramonzon
Add new primer schemas to genome config enhancement Improvement for existing functionality
#472 opened Mar 21, 2025 by saramonzon 2.7
Test latest ivar_variants2vcf script enhancement Improvement for existing functionality
#470 opened Mar 20, 2025 by svarona 2.7
1
Test pipeline results with v2.6.0 and with latest software versions enhancement Improvement for existing functionality
#468 opened Mar 20, 2025 by svarona
6 tasks
2.7
@svarona
Fix nf-core lint enhancement Improvement for existing functionality
#467 opened Mar 20, 2025 by svarona
12 tasks
2.7
Update nf-core modules to the latest software version enhancement Improvement for existing functionality
#466 opened Mar 20, 2025 by svarona
@saramonzon
1
Fix Local Component Structure enhancement Improvement for existing functionality
#465 opened Mar 20, 2025 by svarona
36 tasks
2.7
@cjjossart
Update viralrecon for latest artic minion version enhancement Improvement for existing functionality
#463 opened Mar 20, 2025 by svarona 2.7
@gorbruno
Allow ABACAS for multifasta enhancement Improvement for existing functionality
#461 opened Mar 4, 2025 by svarona 2.7
@reichan1998
Check up if pipeline is up to date with TEMPLATE enhancement Improvement for existing functionality
#449 opened Dec 9, 2024 by maxulysse 2.7
1
Update all local modules to the latest software version enhancement Improvement for existing functionality
#448 opened Dec 5, 2024 by LilyAnderssonLee 2.7
@svarona
2
Addition of a parameter for the minimum depth to call a base enhancement Improvement for existing functionality good first issue Good for newcomers
#447 opened Nov 19, 2024 by cjjossart 2.7
@gorbruno
custom schemes
#445 opened Oct 28, 2024 by rebeelouise 2.7
Pangoli module update: Include pango-designation version enhancement Improvement for existing functionality
#441 opened Sep 4, 2024 by Shettland 2.7
1
Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking bug Something isn't working
#420 opened Feb 27, 2024 by ddomman
6
Properly deal with multiqc in the config files before the next release enhancement Improvement for existing functionality
#411 opened Jan 16, 2024 by maxulysse 2.7
@Joon-Klaps
5
Split authors in generated RO crate enhancement Improvement for existing functionality good first issue Good for newcomers
#404 opened Nov 28, 2023 by renatocjn
Add QIAseq DIRECT SARS-CoV-2 Kit amplicons enhancement Improvement for existing functionality
#394 opened Aug 30, 2023 by dwinter
Artic v5 mismatched primer names in artic-ncov2019 repo cause certain amplicons to be erroneously filtered/removed bug Something isn't working
#392 opened Aug 18, 2023 by Sam-Sims
Minia assembly is non-deterministic in parallel documentation Improvements or additions to documentation enhancement Improvement for existing functionality good first issue Good for newcomers
#381 opened May 11, 2023 by tetedange13
1
2
Add subworkflows to nf-core enhancement Improvement for existing functionality new subworkflow subworkflows
#371 opened Mar 24, 2023 by drpatelh
2 of 5 tasks
Choose Kraken2-filtered host enhancement Improvement for existing functionality
#350 opened Jan 12, 2023 by tetedange13 2.7
3
Update V1200 primer scheme enhancement Improvement for existing functionality
#330 opened Sep 13, 2022 by ddomman 2.7
1
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0