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Hello! Is this bug fixed, or can I ask when this issue will be addressed? I'm interested in obtaining a Bracken result with different levels, and wonder if this issue can be fixed soon. Thanks!
Have you checked the docs?
Description of the bug
bracken output kraken2 style report with recalibrated reads count to a file with rather fixed name pattern (see here for bracken source code ):
new_report + '_bracken_' + abundance_lvl + extension
The
abundance_lvl
is depend on the input parameterbracken -l
(default-l S
), with the mapping rules as follow (also in the same source code):So the current
BRACKEN_BRACKEN
module's output session is not correct, where theabundance_lvl
pattern is fixed.This bug will cause the process throw an error when the
bracken -l
option is not default, eg: using 'S1'Inside the
${workDir}
:See
bracken
worked correctly, but the output filename did not match the pattern so the nf pipeline is stopped.$cat .exitcode 0
Command used and terminal output
No response
Relevant files
No response
System information
No response
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