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53 Open 88 Closed
53 Open 88 Closed
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Issues list

graphtyper error not finding reference
#157 opened Feb 28, 2025 by cahuparo
1
namespaces error with bwa bug Something isn't working
#156 opened Feb 26, 2025 by cahuparo
1
Bakta error, namespaces limit exceed
#155 opened Feb 21, 2025 by cahuparo
1
Change mafft to run in a batch per phylogeny cluster output
#154 opened Feb 20, 2025 by zachary-foster
Make FIND_ASSEMBLIES also parse the JSON result into a table so that not done repeatedly for PICK_ASSEMBLIES
#153 opened Feb 19, 2025 by zachary-foster
Consider combining shared parts of the BUSCO and core gene phylogeny workflows into a single workflow
#152 opened Feb 17, 2025 by zachary-foster
Input data format rework
#150 opened Feb 13, 2025 by zachary-foster
9 tasks
Add an update frequency for stored data
#149 opened Feb 11, 2025 by zachary-foster
.command.sh: line 7: sourmash: command not found
#148 opened Feb 10, 2025 by cahuparo
1
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
ProTip! no:milestone will show everything without a milestone.