8000 port paragraph/idxdepth to nf-test by famosab · Pull Request #8543 · nf-core/modules · GitHub
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port paragraph/idxdepth to nf-test #8543

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Merged
merged 8 commits into from
May 23, 2025
Merged

port paragraph/idxdepth to nf-test #8543

merged 8 commits into from
May 23, 2025
+326 −88

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famosab
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@famosab famosab commented May 23, 2025

PR checklist

Closes #7659

  • 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
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famosab commented May 23, 2025

@nvnieuwk

@SPPearce
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I think we should add an assert that checks if a cram file is being used in conda and fails in that case

@nvnieuwk
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Strange stuff here, maybe the conda version uses a version of HTSLIB that's too old? Could you try specifying a newer version in the environment.yaml file?

@famosab
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famosab commented May 23, 2025

Did not help :(

    > Command error:
    >   [2025-05-23 12:10:39.725] [idxdepth] [1752] [info] BAM: test.paired_end.sorted.cram
    >   [2025-05-23 12:10:39.725] [idxdepth] [1752] [info] Reference: genome.fasta
    >   [2025-05-23 12:10:39.725] [idxdepth] [1752] [info] Output path: test.json
    >   [2025-05-23 12:10:39.725] [idxdepth] [1752] [info] Output path for binned coverage: test.tsv
    >   [E::hts_hopen] Failed to open file test.paired_end.sorted.cram.crai
    >   [E::hts_open_format] Failed to open file "test.paired_end.sorted.cram.crai" : Exec format error
    >   [2025-05-23 12:10:39.726] [idxdepth] [1756] [info] Thread 139931175351872 estimating depth for chr22
    >   [2025-05-23 12:10:39.733] [idxdepth] [1756] [info] Thread 139931175351872 done estimating depth for chr22 ; DP = 0.73 after 7.30496 us
    >   [2025-05-23 12:10:39.733] [idxdepth] [1752] [critical] Assertion failed: indexfile

famosab
famosab commented May 23, 2025
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@nvnieuwk
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nvnieuwk 8000 commented May 23, 2025

Too bad :/ strange that this happens for conda only though... Simon's idea might be the best solution here for now

@famosab
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famosab commented May 23, 2025

I think we should add an assert that checks if a cram file is being used in conda and fails in that case

Did that now - how do we test for this though?

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I think we should add an assert that checks if a cram file is being used in conda and fails in that case

Did that now - how do we test for this though?

Hmm, hard actually to test only on one platform.
I guess either just remove the cram test entirely or turn off the conda testing entirely.

@nvnieuwk
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Did that now - how do we test for this though?

You could run a check to see if the process completes. If it completes, you run the snapshot check, otherwise you check the error message :p

@famosab
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famosab commented May 23, 2025

i think its done @SPPearce @nvnieuwk

@famosab famosab requested a review from SPPearce May 23, 2025 13:59
nvnieuwk
nvnieuwk approved these changes May 23, 2025
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Good job!

@famosab famosab added this pull request to the merge queue May 23, 2025
Merged via the queue into nf-core:master with commit 9e4a2d6 May 23, 2025
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@famosab famosab deleted the para branch May 23, 2025 14:04
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

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nf-test migration: paragraph/idxdepth
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