Description of the bug
Taken from #280
When including bracken in --read_classifiers, the pipeline encounters errors. It appears that the Krona integration step may be reusing scripts designed for Kraken2/Kaiju outputs, which are not fully compatible with Bracken output formats.
It would be helpful to adjust or extend the parsing logic to properly support Bracken results.
2025MA_10F_bracken.tsv
default.command.log
default.command.sh
Command used and terminal output
Relevant files
No response
System information
No response
Description of the bug
Taken from #280
When including bracken in --read_classifiers, the pipeline encounters errors. It appears that the Krona integration step may be reusing scripts designed for Kraken2/Kaiju outputs, which are not fully compatible with Bracken output formats.
It would be helpful to adjust or extend the parsing logic to properly support Bracken results.
2025MA_10F_bracken.tsv
default.command.log
default.command.sh
Command used and terminal output
Relevant files
No response
System information
No response