Gridss environment files / port to nf-test

[famosab]

PR checklist

Closes #5508

• 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.
• Emit the versions.yml file.
• 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

[famosab]

Changes need to be finished after #5933 is merged since that influences the setup section in main.nf.test.

[famosab]

@SPPearce Somehow the versions are not accessed correctly with conda - any idea why?

[SPPearce]

It is failing with an error message before it gets that far

[SPPearce]

https://github.com/nf-core/modules/actions/runs/10634458696/job/29481867188?pr=5932 :

Test Process GRIDSS_SOMATICFILTER

  Test [40d75c38] 'human - vcf' 
    > N E X T F L O W  ~  version 24.04.4
    > Launching `/opt/actions-runner/_work/modules/modules/.nf-test-40d75c3865392257efc32c38a8ae25a2.nf` [hopeful_sammet] DSL2 - revision: 52fa2580f4
    > Creating env using conda: /opt/actions-runner/_work/modules/modules/modules/nf-core/gridss/somaticfilter/tests/../../../bwa/index/environment.yml [cache /home/ubuntu/tests/40d75c3865392257efc32c38a8ae25a2/work/conda/bwa_index-e04957aeeb5615827c[51](https://github.com/nf-core/modules/actions/runs/10634458696/job/29481867188?pr=5932#step:14:52)54[52](https://github.com/nf-core/modules/actions/runs/10634458696/job/29481867188?pr=5932#step:14:53)1bb90048]
    > [6a/7c4040] Submitted process > BWA_INDEX (genome.fasta)
    > WARN: Input tuple does not match tuple declaration in process `GRIDSS_GRIDSS` -- offending value: [[id:test], /nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam, []]
    > Creating env using conda: /opt/actions-runner/_work/modules/modules/modules/nf-core/gridss/somaticfilter/tests/../../../gridss/gridss/environment.yml [cache /home/ubuntu/tests/40d75c386[53](https://github.com/nf-core/modules/actions/runs/10634458696/job/29481867188?pr=5932#step:14:54)92257efc32c38a8ae25a2/work/conda/gridss_gridss-716d62033d0cd1f43531d3f9d4d204fe]
    > [6f/83bdfb] Submitted process > GRIDSS_GRIDSS (test)
    > Creating env using conda: /opt/actions-runner/_work/modules/modules/modules/nf-core/gridss/somaticfilter/tests/../environment.yml [cache /home/ubuntu/tests/40d75c3865392257efc32c38a8ae25a2/work/conda/gridss_somaticfilter-179f560e4ee1afe2a0c14c43fb3ca9dc]
    > [f2/21a256] Submitted process > GRIDSS_SOMATICFILTER (test)
    > ERROR ~ Error executing process > 'GRIDSS_SOMATICFILTER (test)'
    > 
    > Caused by:
    >   Process `GRIDSS_SOMATICFILTER (test)` terminated with an error exit status (1)
    > 
    > 
    > Command executed:
    > 
    >   gridss_somatic_filter \
    >       --input test.vcf.gz \
    >        \
    >       --output test.high_confidence_somatic.vcf \
    >       --fulloutput test.all_somatic.vcf \
    >       --normalordinal 0
    >   
    >   cat <<-END_VERSIONS > versions.yml
    >   "GRIDSS_SOMATICFILTER":
    >       gridss: 2.13.2
    >   END_VERSIONS
    > 
    > Command exit status:
    >   1
    > 
    > Command output:
    >   Test passed 🌈
    >   Test passed 🥇
    > 
    > Command error:
    >   Attaching package: ‘Matrix’
    >   
    >   The following object is masked from ‘package:S4Vectors’:
    >   
    >       expand
    >   
    >   The following objects are masked from ‘package:tidyr’:
    >   
    >       expand, pack, unpack
    >   
    >   
    >   Attaching package: ‘MatrixGenerics’
    >   
    >   The following objects are masked from ‘package:matrixStats’:
    >   
    >       colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    >       colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    >       colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    >       colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    >       colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    >       colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    >       colWeightedMeans, colWeightedMedians, colWeightedSds,
    >       colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    >       rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    >       rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    >       rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    >       rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    >       rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    >       rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    >       rowWeightedSds, rowWeightedVars
    >   
    >   
    >   Attaching package: ‘S4Arrays’
    >   
    >   The following object is masked from ‘package:abind’:
    >   
    >       abind
    >   
    >   The following object is masked from ‘package:base’:
    >   
    >       rowsum
    >   
    >   Test passed 🌈
    >   Test passed 🥇
    >   No reference genome supplied using --ref. Not performing variant equivalence checks.
    >   2024-08-30 14:52:[55](https://github.com/nf-core/modules/actions/runs/10634458696/job/29481867188?pr=5932#step:14:56).635999 Reading test.vcf.gz
    >   Tumour samples: 
    >   Matched normals: 
    >   Error: array-like subscript has more than one effective dimension
    >   Execution halted
    >   

worth noting it is complaining that the tuple doesn't match at the top:
> WARN: Input tuple does not match tuple declaration in processGRIDSS_GRIDSS -- offending value: [[id:test], /nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam, []]

[famosab]

I am also confused by the error message. I tried running it locally but that did not work because of the M1 chip and then I did not have any more time to configure that the run with conda works.

[SPPearce]

I just use gitpod for all my development work, has all three container engines available