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46 Open 77 Closed
46 Open 77 Closed
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Issues list

ERROR: AMRFinderPlus failed! command: 'amrfinder_update --force_update --database db/amrfinderplus-db', error code: 1 bug Something isn't working
#139 opened Jan 30, 2025 by cahuparo
2
Support 454 or see how to handle them enhancement New feature or request
#138 opened Jan 30, 2025 by cahuparo
Error executing process > 'PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK bug Something isn't working
#137 opened Jan 29, 2025 by cahuparo
3
FIND_ASSEMBLIES returns error code when no results are found bug Something isn't working good first issue Good for newcomers
#133 opened Jan 14, 2025 by zachary-foster
BWA. paired reads have different names: "SRR1655713.931913", "SRR1655713.3"
#132 opened Dec 30, 2024 by cahuparo
1
Additional IQTREE2 issue-bootstrap error when less than 4 samples bug Something isn't working
#129 opened Dec 18, 2024 by masudermann
Can't to pick contextual reference for validation dataset.
#127 opened Dec 16, 2024 by cahuparo
Use NCBI metadata for defualt coloring of plots
#125 opened Dec 3, 2024 by zachary-foster
IQ-tree SNP error
#124 opened Dec 3, 2024 by buchanri
2
Error if users give percentages to arguments that require proportions
#123 opened Dec 2, 2024 by zachary-foster
Replace VCF_TO_TAB and VCF_TO_SNPALN with a single R script or other command
#122 opened Nov 21, 2024 by zachary-foster
ASSIGN_CONTEXT_REFERENCES error
#121 opened Nov 21, 2024 by cahuparo
1
Consider changing MSN threshold to number of SNPs
#120 opened Nov 19, 2024 by zachary-foster
Add scale bars to trees
#119 opened Nov 19, 2024 by zachary-foster
BUSCO error = BrokenPipeError: [Errno 32] Broken pipe
#118 opened Nov 19, 2024 by cahuparo
Name dropdown entires for MSN by reference taxon name
#117 opened Nov 18, 2024 by zachary-foster
Consider the abundance of the taxon when choosing references.
#116 opened Nov 18, 2024 by zachary-foster
Add option to specify number of replicates when downloading references
#115 opened Nov 18, 2024 by zachary-foster
accept assemblies as well as reads
#114 opened Nov 8, 2024 by cahuparo
Switch from entrez commands to datasets commands for downloading assembly metadata
#113 opened Nov 7, 2024 by zachary-foster
Out of date spades may be causing errors with assemblies bug Something isn't working
#109 opened Nov 4, 2024 by cahuparo
2
Double quotes in queries in input causes parsing errors with the new nf-core template bug Something isn't working
#108 opened Oct 31, 2024 by zachary-foster
Add module to check quality of Spades assembly
#105 opened Oct 28, 2024 by logankblair
Change assign_context_references.R to give more informative error message
#104 opened Oct 28, 2024 by logankblair
Failed rendering report
#103 opened Oct 23, 2024 by buchanri
2
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