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48 Open 84 Closed
48 Open 84 Closed
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Issues list

.command.sh: line 7: sourmash: command not found
#148 opened Feb 10, 2025 by cahuparo
1
Consider combining sample and reference metdata into a single sheet
#147 opened Feb 9, 2025 by zachary-foster
Track original row number in sample data sheet for reporting errors to the user
#146 opened Feb 9, 2025 by zachary-foster
Add option to error and stop execution instead of issuing warnings when checking sample sheet
#145 opened Feb 8, 2025 by zachary-foster
With dorado correct producing fasta read files, could the pipeline take fasta files as input? enhancement New feature or request
#144 opened Feb 7, 2025 by cahuparo
Set enable = FALSE instead of erroring when reasonable in check_samplesheet.R
#143 opened Feb 7, 2025 by zachary-foster
Handle biosamples that are assocaited with assemblies instead of reads
#142 opened Feb 6, 2025 by zachary-foster
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
1
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
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
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
Add module to check quality of Spades assembly
#105 opened Oct 28, 2024 by logankblair
ProTip! Adding no:label will show everything without a label.