Update adapterremoval

[angelphanth]

PR checklist

Closes #10143

• followed: https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules
  This pull request updates the AdapterRemoval module to use version 2.3.4 and refactors how software version information is captured and output, moving away from file-based reporting to a more structured tuple-based approach. It also cleans up and clarifies metadata and test handling, ensuring better consistency and future extensibility.

AdapterRemoval version update:

• Updated the AdapterRemoval tool from version 2.3.2 to 2.3.4 in both the conda environment (environment.yml) and container image references in the process definition (main.nf). [1] [2]

Refactoring version reporting:

• Replaced the output of a versions.yml file with a new tuple-based output channel (versions_AdapterRemoval) that directly reports the process name, tool name, and version string. This change is reflected in both the process output definition and the process script, removing the block of code that generated versions.yml. [1] [2] [3] [4]

Metadata and schema improvements:

• Updated meta.yml to clarify and expand tool metadata, input/output descriptions, and ontologies. Added a new schema for versions_AdapterRemoval and modernized the general versions topic to match the new tuple-based approach. [1] [2] [3] [4] [5] [6] [7] [8] [9]

Test updates:

• Updated tests to expect the new tuple-based version output instead of the previous versions.yml file, searching for outputs with keys starting with "versions". [1] [2] [3] [4] [5] [6] [7]

• Updated test snapshots to match the new output structure and updated tool version, and to reflect changes in metadata and Nextflow/nf-test versions. [1] [2] [3] [4] [5] [6]

• This comment contains a description of changes (with reason).

• If you've fixed a bug or added code that should be tested, add tests!

• If you've added a new tool - have you followed the module conventions in the contribution docs

• If necessary, include test data in your PR.

• Remove all TODO statements.

• Broadcast software version numbers to topic: versions - See version_topics

• Follow the naming conventions.

• Follow the parameters requirements.

• Follow the input/output options guidelines.

• Add a resource label

• Use BioConda and BioContainers if possible to fulfil software requirements.

• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:

  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[vagkaratzas]

Remove the ADAPTERREMOVAL versions from the downstream subworkflows:
FASTQ_REMOVEADAPTERS_MERGE and FASTQ_SHORTREADS_PREPROCESS_QC and re-run their nf-tests to make sure nothing breaks :D

[angelphanth]

Remove the ADAPTERREMOVAL versions from the downstream subworkflows: FASTQ_REMOVEADAPTERS_MERGE and FASTQ_SHORTREADS_PREPROCESS_QC and re-run their nf-tests to make sure nothing breaks :D

the test that is failing : "sarscov2 - fastq - bbduk - paired-end"

  [e5/0c717f] Submitted process > FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)
  ERROR ~ Error executing process > 'FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)'
  
  Caused by:
    Process `FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)` terminated with an error exit status (1)
  
  
  Command executed:
  
    bbduk.sh \
        -Xmx4g \
        in1=test_1.fastq.gz in2=test_2.fastq.gz \
        out1=test_bbduk_1.fastq.gz out2=test_bbduk_2.fastq.gz \
        threads=2 \
        trimq=10 qtrim=r \
         \
        &> test_bbduk.bbduk.log
    
    cat <<-END_VERSIONS > versions.yml
    "FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK":
        bbmap: $(bbversion.sh | grep -v "]")
    END_VERSIONS
  
  Command exit status:
    1
  
  Command output:
    (empty)

[angelphanth]

Remove the ADAPTERREMOVAL versions from the downstream subworkflows: FASTQ_REMOVEADAPTERS_MERGE and FASTQ_SHORTREADS_PREPROCESS_QC and re-run their nf-tests to make sure nothing breaks :D

the test that is failing : "sarscov2 - fastq - bbduk - paired-end"

  [e5/0c717f] Submitted process > FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)
  ERROR ~ Error executing process > 'FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)'
  
  Caused by:
    Process `FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK (test_bbduk)` terminated with an error exit status (1)
  
  
  Command executed:
  
    bbduk.sh \
        -Xmx4g \
        in1=test_1.fastq.gz in2=test_2.fastq.gz \
        out1=test_bbduk_1.fastq.gz out2=test_bbduk_2.fastq.gz \
        threads=2 \
        trimq=10 qtrim=r \
         \
        &> test_bbduk.bbduk.log
    
    cat <<-END_VERSIONS > versions.yml
    "FASTQ_REMOVEADAPTERS_MERGE:BBMAP_BBDUK":
        bbmap: $(bbversion.sh | grep -v "]")
    END_VERSIONS
  
  Command exit status:
    1
  
  Command output:
    (empty)

fixed this by increasing the size of my VM e.g.

colima start --cpu 4 --memory 8

:)

[vagkaratzas]

Ready! Nice!