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DSL2: nf-test conversion test_full #1159

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TCLamnidis
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PR checklist

  • 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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@TCLamnidis TCLamnidis changed the base branch from master to dev September 26, 2025 09:50
@nf-core nf-core deleted a comment from github-actions bot Sep 26, 2025
@TCLamnidis
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TCLamnidis commented Sep 26, 2025 •
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Due to the long runtime of this test, I decided to move it to the EVA cluster, but I cannot get FastQC to run successfully there :/

Here's the error for future reference:

ERROR ~ Error executing process > 'NFCORE_EAGER:EAGER:FASTQC (COD076_COD076E1bL1_L8)'
  
  Caused by:
    Process `NFCORE_EAGER:EAGER:FASTQC (COD076_COD076E1bL1_L8)` terminated with an error exit status (1)
  
  
  Command executed:
  
    printf "%s %s\n" ERR1943600_1.fastq.gz COD076_COD076E1bL1_L8_1.gz ERR1943600_2.fastq.gz COD076_COD076E1bL1_L8_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done
    
    fastqc \
        --quiet \
        --threads 4 \
        --memory 2048 \
        COD076_COD076E1bL1_L8_1.gz COD076_COD076E1bL1_L8_2.gz
    
    cat <<-END_VERSIONS > versions.yml
    "NFCORE_EAGER:EAGER:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
  
  Command exit status:
    1
  
  Command output:
    Error occurred during initialization of VM
    Could not reserve enough space for 8388608KB object heap
  
  Command error:
    Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=1
  
  Work dir:
    /r1/people/thiseas_christos_lamnidis/Software/github/nf-core/eager/.nf-test/tests/8a6454f4b1554876bfdb1b4fe8c623ec/work/56/a09f0a65a6f9310ce319262d11847d
  
  Container:
    /mnt/archgen/tools/singularity/containers/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img
  
  Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
  
   -- Check '/r1/people/thiseas_christos_lamnidis/Software/github/nf-core/eager/.nf-test/tests/8a6454f4b1554876bfdb1b4fe8c623ec/meta/nextflow.log' file for details
  ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
  
   -- Check '/r1/people/thiseas_christos_lamnidis/Software/github/nf-core/eager/.nf-test/tests/8a6454f4b1554876bfdb1b4fe8c623ec/meta/nextflow.log' file for details
  Nextflow stderr:

I tried increasing the memory of FastQC, and decreasing the number of cores (the module does a memory/cores division to keep Java in check), but to no avail.

@TCLamnidis
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TCLamnidis commented Oct 10, 2025 •
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Update. It seems that the process resources specified in the test_full config get overwritten by the cluster defaults (since running nf-test test --profile=+eva,archgen --tag test_full --update-snapshot indeed will load the test_full profile first, THEN the eva and archgen ones.

Sadly, there is no way to tweak the profile order in nf-test: https://www.nf-test.com/docs/configuration/#managing-profiles
CLI profiles will ALWAYS overwrite those provided in the test itself.

I tried adding test_full to the CLI profiles, kepeing the +, and that failed. I resorted to using nf-test test --profile=eva,archgen,test_full --tag test_full --update-snapshot, and ignoring the test's internal profile definition. This should work locally, and in th eCI, there will be no eva,archgen profiles to cause this issue. 🤞

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@TCLamnidis
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