Incorrect BRACKEN_BRACKEN output session

[MajoroMask]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

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 parameter bracken -l (default -l S), with the mapping rules as follow (also in the same source code):

#Abundance level
    lvl_dict = {}
    lvl_dict['D'] = 'domains'
    lvl_dict['P'] = 'phylums'
    lvl_dict['O'] = 'orders'
    lvl_dict['C'] = 'classes'
    lvl_dict['F'] = 'families'
    lvl_dict['G'] = 'genuses' 
    lvl_dict['S'] = 'species'
    abundance_lvl = args.level
    if args.level in lvl_dict:
        abundance_lvl = lvl_dict[args.level]

So the current BRACKEN_BRACKEN module's output session is not correct, where the abundance_lvl pattern is fixed.

    output:
    tuple val(meta), path(bracken_report)        , emit: reports
    tuple val(meta), path("*bracken_species.txt"), emit: txt  // HERE!
    path "versions.yml"          , emit: versions

This bug will cause the process throw an error when the bracken -l option is not default, eg: using 'S1'

Error executing process > 'BRACKEN_BRACKEN (2613_pe - virus - S1)'

Caused by:
[49/e36e7c] Submitted process > BRACKEN_BRACKEN (2613_pe - virus - S1)
  Missing output file(s) `*bracken_species.txt` expected by process `BRACKEN_BRACKEN (2613_pe - virus - S1)`

Inside the ${workDir}:

$ls -alhn
total 52K
drwxrwxr-x    2 1008     1008        4.0K Oct 27 03:11 .
drwxrwxr-x    4 1008     1008          94 Oct 27 03:11 ..
-rw-rw-r--    1 1008     1008           0 Oct 27 03:11 .command.begin
-rw-rw-r--    1 1008     1008          65 Oct 27 03:11 .command.err
-rw-rw-r--    1 1008     1008         938 Oct 27 03:11 .command.log
-rw-rw-r--    1 1008     1008         873 Oct 27 03:11 .command.out
-rw-rw-r--    1 1008     1008       10.1K Oct 27 03:11 .command.run
-rw-rw-r--    1 1008     1008         285 Oct 27 03:11 .command.sh
-rw-r--r--    1 1008     0            201 Oct 27 03:11 .command.trace
-rw-rw-r--    1 1008     1008           1 Oct 27 03:11 .exitcode
lrwxrwxrwx    1 1008     1008          60 Oct 27 03:11 20230926_virus -> /data/databases/bracken/20230926_virus
lrwxrwxrwx    1 1008     1008         103 Oct 27 03:11 2613_pe_standardized.kraken2.report.txt -> /proj/pipeline/work/e6/df555c1f09531369b3a507f38ddca2/2613_pe_standardized.kraken2.report.txt
-rw-r--r--    1 1008     0           3.1K Oct 27 03:11 2613_pe_standardized.kraken2.report_bracken_S1.txt
-rw-r--r--    1 1008     0            804 Oct 27 03:11 2613_pe_virus.S1.bracken.tsv
-rw-r--r--    1 1008     0             61 Oct 27 03:11 versions.yml

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

[youngje-cs-cmu]

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!