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Issues list

Potentially replace cutadapt with seqkit amplicon to simplify primer processing enhancement New feature or request
#30 opened Oct 14, 2024 by nrminor
Workaround for iVar not outputting separate reference segments in consensus sequences bug Something isn't working enhancement New feature or request help wanted Extra attention is needed
#25 opened Sep 30, 2024 by nrminor
Fix the process that checks the validity of a requested nextclade dataset bug Something isn't working
#23 opened Sep 24, 2024 by nrminor
Refactor so that one incomplete/unreconciled primer pair does not crash the whole run and instead allows it to proceed with what primer pairs it has bug Something isn't working enhancement New feature or request help wanted Extra attention is needed
#22 opened Sep 24, 2024 by nrminor
Add a subworkflow that bundles results for upload to SRA, Genbank, and GISAID enhancement New feature or request help wanted Extra attention is needed
#20 opened Sep 24, 2024 by nrminor
Make sure the illumina workflow has remained up to date now that the nanopore workflow has gone through many feature adds help wanted Extra attention is needed
#19 opened Sep 24, 2024 by nrminor
Enable optional email-notification-based workflow reporting enhancement New feature or request
#16 opened Sep 6, 2024 by nrminor
Add reference-free branch of the pipeline that takes primer sequences alone rather than required a reference and a bed file enhancement New feature or request help wanted Extra attention is needed
#15 opened Sep 5, 2024 by nrminor
Add final variant long- and pivot-table for assessing amino acid variants across samples enhancement New feature or request
#14 opened Sep 5, 2024 by nrminor
Add more exhaustive setup instructions for local and HPC execution (and eventually cloud?) documentation Improvements or additions to documentation
#11 opened Jul 10, 2024 by nrminor
@nrminor
Complete developer guide documentation Improvements or additions to documentation
#10 opened Jul 10, 2024 by nrminor
Fix amplicon counting to enable grouping by sample when using .watchPath() bug Something isn't working
#8 opened Jun 28, 2024 by nrminor
@nrminor
Primer resplicing improvements bug Something isn't working enhancement New feature or request help wanted Extra attention is needed
#5 opened Jun 28, 2024 by nrminor
Barcode sample id lookup enhancement New feature or request
#4 opened Jun 28, 2024 by nrminor
@nrminor
ARM compatibility bug Something isn't working
#3 opened Jun 28, 2024 by ajlail98
@nrminor
1
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