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34 Open 133 Closed
34 Open 133 Closed
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Issues list

Check up if pipeline is up to date with TEMPLATE enhancement Improvement for existing functionality
#449 opened Dec 9, 2024 by maxulysse
Update all modules to the latest enhancement Improvement for existing functionality
#448 opened Dec 5, 2024 by LilyAnderssonLee 2.7
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
custom schemes
#445 opened Oct 28, 2024 by rebeelouise
Include pango-designation version enhancement Improvement for existing functionality
#441 opened Sep 4, 2024 by Shettland
variant discrepancy between in ivar and snpeff annotated file bug Something isn't working
#429 opened May 13, 2024 by wantingwei 2.7
2
Error when running illumina command bug Something isn't working
#423 opened Apr 8, 2024 by fractaljc
nf-core/viralrecon run halted due to R version clash
#422 opened Mar 24, 2024 by asanenjoy
6
Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking bug Something isn't working
#420 opened Feb 27, 2024 by ddomman
5
Temp file problem in VARIANTS_IVAR:BCFTOOLS_SORT bug Something isn't working
#415 opened Jan 30, 2024 by Paururo
1
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
3
Split authors in generated RO crate enhancement Improvement for existing functionality
#404 opened Nov 28, 2023 by renatocjn
Error running version 2.6.0 with Nanopore data in process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION bug Something isn't working
#402 opened Oct 31, 2023 by AdrianMBarrera
Problem installing viralrecon bug Something isn't working
#399 opened Oct 13, 2023 by vilocha
Argument input-fasta is missing in NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:NEXTCLADE_RUN" bug Something isn't working
#398 opened Oct 12, 2023 by CeliaRodrigues
4
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
[bug] Fails to find FASTQ files when stored on S3 bug Something isn't working
#385 opened Jul 31, 2023 by adamrtalbot
@maxulysse
ERROR ~ Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION' bug Something isn't working
#383 opened Jun 28, 2023 by alethomas
1
Minimum frequency threshold is being ignored bug Something isn't working
#382 opened Jun 6, 2023 by AndreaAguadoM
2
Minia assembly is non-deterministic in parallel enhancement Improvement for existing functionality
#381 opened May 11, 2023 by tetedange13
1
ERROR picard container for NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS -> setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory bug Something isn't working
#379 opened Apr 19, 2023 by grendon
2
-[nf-core/viralrecon] Pipeline completed with errors- Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518)' Caused by: Process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518) terminated with an error exit status (20) bug Something isn't working
#376 opened Mar 31, 2023 by dejenie21
3
Add support for artic primer set version V5.3.2 enhancement Improvement for existing functionality
#373 opened Mar 24, 2023 by mbdabrowska1
11
Add subworkflows to nf-core enhancement Improvement for existing functionality new subworkflow subworkflows
#371 opened Mar 24, 2023 by drpatelh
2 of 5 tasks
@Joon-Klaps
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