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381 Open 786 Closed
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Issues list

Request: Make MultiQC 1.24.1+galaxy0 custom parsing backwards compatible with 1.11+galaxy1
#6335 opened Sep 16, 2024 by jennaj
JupyLab Tool Issues
#6326 opened Sep 13, 2024 by nomadscientist
2
Request: add in option to write out headers in dnadiff outputs
#6325 opened Sep 12, 2024 by jennaj
Request: add more to the Help section for dnadiff
#6319 opened Sep 10, 2024 by jennaj
Bug with gffread: converting gff3 to gtf results in transcript lines missing the final ;
#6310 opened Sep 6, 2024 by jennaj
ToolTemplatingException: Error occurred while building config files for tool 'scanpy_plot/1.9.6+galaxy4' affects UseGalaxy.* kind/bug
#6302 opened Sep 4, 2024 by galaxyproject-sentryintegration bot
1
trinity_align_and_estimate_abundance tool dependency issue
#6298 opened Sep 4, 2024 by sanjaysrikakulam
tracegroomer: output options & citation
#6294 opened Sep 3, 2024 by johaGL
5 tasks done
1
gProfiler tool update
#6286 opened Aug 29, 2024 by Mennayousef
2
-z parameter in RAxML, or new tool request: RAxML-NG
#6230 opened Aug 12, 2024 by Hymenium
Tool Request: Single cell tool request
#6219 opened Aug 9, 2024 by nomadscientist
1
Table Compute: Wanted Features
#6201 opened Aug 2, 2024 by mtekman
4 tasks
4
BUSCO default parameter not handled accurately
#6200 opened Aug 1, 2024 by SaimMomin12
fasterq_dump misses the clip option
#6171 opened Jul 23, 2024 by paulzierep
2
Diamond: optional outputs produced do not respect tool form settings
#6170 opened Jul 22, 2024 by jennaj
1
@bgruening
Tool Request: HERRO tool request
#6166 opened Jul 21, 2024 by jessemartin132
Update kraken-related tools to enable use of both Kraken and Kraken2 indexes
#6160 opened Jul 17, 2024 by jennaj
2 tasks
1
Idea: Add test cases to DMs that checks if all remote urls exist
#6151 opened Jul 15, 2024 by paulzierep
BUSCO --miniprot parameter seems incorrectly handled
#6147 opened Jul 14, 2024 by Hymenium
1
add new tool pyclone-vi tool request
#6143 opened Jul 12, 2024 by bdartigues
Unclear explanation and options for Funannotate --augustus_species parameter
#6137 opened Jul 8, 2024 by Hymenium
2
goenrichment ignores JAVA_OPTS and JAVA_TOOL_OPTIONS
#6135 opened Jul 8, 2024 by martindemko
2
BUSCO gff file(s) not captured in output when Augustus used, no errors as stderr suppressed
#6132 opened Jul 8, 2024 by Hymenium
Bug in ampvis2 tax_show
#6126 opened Jul 4, 2024 by paulzierep
2
Tool Request: Plugin: Adding nonsense mediated decay (NMD) plugin to ensembl_vep tool request
#6122 opened Jul 2, 2024 by prao123
1
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