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Bactopia v4 - Overview & Help Wanted

v4

Status: Open.

#628 In bactopia/bactopia;

· rpetit3 opened on Aug 5, 2025

[enhancement] - Update workflows for Nextflow Strict syntax

Status: Open.

#627 In bactopia/bactopia;

· rpetit3 opened on Aug 5, 2025

[feature] Bactopia Summary support for clean-yer-reads

enhancementNew feature or requestNew feature or request

v4

Status: Open.

#626 In bactopia/bactopia;

· coxrs opened on Jul 25, 2025

[question] Stuck at QC module when short polishing longreads

questionFurther information is requestedFurther information is requested

v4

Status: Open.

#625 In bactopia/bactopia;

· Jluvin opened on Jul 13, 2025

[bug] bactopia fails upon estimating genome size using kmc

bugSomething isn't workingSomething isn't working

v4

Status: Open.

#624 In bactopia/bactopia;

· donEnno opened on Jul 11, 2025

[question] MLST calls using different scheme and no call for K. pneumonia

questionFurther information is requestedFurther information is requested

v4

Status: Open.

#622 In bactopia/bactopia;

· coxrs opened on Jun 24, 2025

[bug] Process <code>BACTOPIA:DUMPSOFTWAREVERSIONS (1)</code> terminated with an error exit status (1)

bugSomething isn't workingSomething isn't working

v4

Status: Open.

#621 In bactopia/bactopia;

· Svnipni opened on Jun 19, 2025

error running bactopia -profile test,docker

bugSomething isn't workingSomething isn't working

v4

Status: Open.

#620 In bactopia/bactopia;

· JavariaAshraf opened on Jun 19, 2025

[question]Running PIRATE on Bakta Output

questionFurther information is requestedFurther information is requested

v4

Status: Open.

#619 In bactopia/bactopia;

· whottel opened on Jun 12, 2025

[bug] Process <code>BACTOPIATOOLS:PANGENOME:PG_TOOL:PIRATE_MODULE</code> input file name collision -- There are multiple input files for each of the following file names

bugSomething isn't workingSomething isn't working

v4

Status: Open.

#618 In bactopia/bactopia;

· aperreault opened on Jun 12, 2025

[bug] SKESA OOM Failure Reporting

bugSomething isn't workingSomething isn't working

v4

Status: Open.

#617 In bactopia/bactopia;

· wtporter opened on Jun 10, 2025

[question] Using mashtree with bactopia results for local files AND taxid sample

questionFurther information is requestedFurther information is requested

v4

Status: Open.

#616 In bactopia/bactopia;

· aperreault opened on Jun 10, 2025