SAM2LCA_UPDATEDB error with nf-test conda | 25.04.0

Description of the bug

> [88/a73138] Submitted process > SAM2LCA_UPDATEDB (test)
> ERROR ~ Error executing process > 'SAM2LCA_UPDATEDB (test)'
> 
> Caused by:
>   Process `SAM2LCA_UPDATEDB (test)` terminated with an error exit status (1)
> 
> 
> Command executed:
> 
>   mkdir -p sam2lca_db
>   
>   sam2lca -d sam2lca_db \
>       update-db \
>       -t test \
>        \
>        \
>        \
>       -a test \
>        \
>   
>   
>   cat <<-END_VERSIONS > versions.yml
>   "SAM2LCA_UPDATEDB":
>       sam2lca: $(echo $(sam2lca --version 2>&1) | sed 's/^sam2lca, version //' )
>   END_VERSIONS
> 
> Command exit status:
>   1
> 
> Command output:
>   (empty)
> 
> Command error:
>   Traceback (most recent call last):
>     File "/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/bin/sam2lca", line 7, in <module>
>       from sam2lca.cli import cli
>     File "/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/__init__.py", line 3, in <module>
>       from sam2lca.main import sam2lca
>     File "/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/main.py", line 5, in <module>
>       from sam2lca.taxonomy import setup_taxopy_db, load_taxonomy_db
>     File "/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/taxonomy.py", line 1, in <module>
>       from pkg_resources import ExtractionError
>   ModuleNotFoundError: No module named 'pkg_resources'
> 
> Work dir:
>   /home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/88/a73138ebcb343824f0368fc01f475c
> 
> Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
> 
>  -- Check '/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/meta/nextflow.log' file for details
> Execution cancelled -- Finishing pending tasks before exit

Assertion failed:

assert process.success
| |
| false
SAM2LCA_UPDATEDB

FAILED (39.789s)

Assertion failed:

1 of 1 assertions failed

Nextflow stdout:

N E X T F L O W ~ version 25.04.0
Launching /home/runner/_work/coproid/coproid/.nf-test-b522f1b3c269e266700d329555d7988b.nf [trusting_mahavira] DSL2 - revision: e13a77db57
Downloading plugin nf-schema@2.5.1
Creating env using conda: /home/runner/_work/coproid/coproid/modules/local/sam2lca/updatedb/environment.yml [cache /home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e]
[88/a73138] Submitted process > SAM2LCA_UPDATEDB (test)
ERROR ~ Error executing process > 'SAM2LCA_UPDATEDB (test)'

Caused by:
Process SAM2LCA_UPDATEDB (test) terminated with an error exit status (1)

Command executed:

mkdir -p sam2lca_db

sam2lca -d sam2lca_db \
    update-db \
    -t test \
     \
     \
     \
    -a test \
     \


cat <<-END_VERSIONS > versions.yml
"SAM2LCA_UPDATEDB":
    sam2lca: $(echo $(sam2lca --version 2>&1) | sed 's/^sam2lca, version //' )
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File "/home/runner/_work/coproid/coproid//tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/bin/sam2lca", line 7, in
from sam2lca.cli import cli
File "/home/runner/_work/coproid/coproid//tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/init.py", line 3, in
from sam2lca.main import sam2lca
File "/home/runner/_work/coproid/coproid//tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/main.py", line 5, in
from sam2lca.taxonomy import setup_taxopy_db, load_taxonomy_db
File "/home/runner/_work/coproid/coproid//tests/b522f1b3c269e266700d329555d7988b/work/conda/env-cb576d7291abe96e-93f808b205f3b8d30fb148c1f88e224e/lib/python3.12/site-packages/sam2lca/taxonomy.py", line 1, in
from pkg_resources import ExtractionError
ModuleNotFoundError: No module named 'pkg_resources'

Work dir:
/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/work/88/a73138ebcb343824f0368fc01f475c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '/home/runner/_work/coproid/coproid/~/tests/b522f1b3c269e266700d329555d7988b/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Nextflow 25.10.4 is available - Please consider updating your version to it

FAILURE: Executed 1 tests in 39.794s (1 failed)

Command used and terminal output

Relevant files

No response

System information

No response

The failing process uses modules/local/sam2lca/updatedb/environment.yml; start by inspecting that environment definition and reproduce the SAM2LCA_UPDATEDB nf-test. Confirm the environment provides the dependency required by sam2lca so the test completes without the pkg_resources error.