port parabricks/deepvariant to nf-test

[famosab]

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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  • 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]

Currently assessing the created g.vcf always fails with

╭────────────────────────────────────────────────────────────────────────────────────────────────────────────── nf-test error ───────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ groovy.lang.MissingMethodException: No signature of method: static com.askimed.nf.test.lang.extensions.GlobalMethods.file() is applicable for argument types: (ArrayList) values: [[/home/paifb01/modules/.nf-test/tests/2608642d653b0463a │
│ Possible solutions: file(java.lang.String), find(), find(groovy.lang.Closure), use([Ljava.lang.Object;), with(groovy.lang.Closure), is(java.lang.Object)                                                                                   │
│                                                                                                                                                                                                                                            │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

[famosab]

Now the runners are picking up and some of the tests pass but some do not. Locally everything looks fine:

 nf-core modules test parabricks/deepvariant -u --profile docker


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.0.2 - https://nf-co.re
    There is a new version of nf-core/tools available! (3.1.1)


INFO     Generating nf-test snapshot                                                                                                                                            
╭─────────────────────────────────────────────────────────────────────────────── nf-test output ───────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                              │
│ 🚀 nf-test 0.9.2                                                                                                                                                             │
│ https://www.nf-test.com                                                                                                                                                      │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                                         │
│                                                                                                                                                                              │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                                                                                        │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                                                                                              │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                                        │
│ Warning: every snapshot that fails during this test run is re-record.                                                                                                        │
│                                                                                                                                                                              │
│ Test Process PARABRICKS_DEEPVARIANT                                                                                                                                          │
│                                                                                                                                                                              │
│   Test [d4150cc7] 'human - bam' PASSED (19.026s)                                                                                                                             │
│   Test [7915f0a7] 'human - bam - intervals' PASSED (18.794s)                                                                                                                 │
│   Test [4a9986c1] 'human - bam - gvcf' PASSED (22.216s)                                                                                                                      │
│   Test [2608642d] 'human - bam - intervals - gvcf' PASSED (17.976s)                                                                                                          │
│   Test [92648df2] 'human - bam - stub' PASSED (10.546s)                                                                                                                      │
│   Test [cd720ada] 'human - bam - intervals - gvcf - stub' PASSED (13.86s)                                                                                                    │
│                                                                                                                                                                              │
│                                                                                                                                                                              │
│ SUCCESS: Executed 6 tests in 102.508s                                                                                                                                        │
│                                                                                                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability                                                                                                                   
╭─────────────────────────────────────────────────────────────────────────────── nf-test output ───────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                              │
│ 🚀 nf-test 0.9.2                                                                                                                                                             │
│ https://www.nf-test.com                                                                                                                                                      │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                                         │
│                                                                                                                                                                              │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                                                                                        │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                                                                                              │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                                        │
│                                                                                                                                                                              │
│ Test Process PARABRICKS_DEEPVARIANT                                                                                                                                          │
│                                                                                                                                                                              │
│   Test [d4150cc7] 'human - bam' PASSED (20.539s)                                                                                                                             │
│   Test [7915f0a7] 'human - bam - intervals' PASSED (17.475s)                                                                                                                 │
│   Test [4a9986c1] 'human - bam - gvcf' PASSED (16.655s)                                                                                                                      │
│   Test [2608642d] 'human - bam - intervals - gvcf' PASSED (18.481s)                                                                                                          │
│   Test [92648df2] 'human - bam - stub' PASSED (10.007s)                                                                                                                      │
│   Test [cd720ada] 'human - bam - intervals - gvcf - stub' PASSED (9.339s)                                                                                                    │
│                                                                                                                                                                              │
│                                                                                                                                                                              │
│ SUCCESS: Executed 6 tests in 92.639s                                                                                                                                         │
│                                                                                                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed! 

[SPPearce]

The runners seem to be giving a different md5sum for the path(process.out.vcf[0][1]).vcf.variantsMD5

[SPPearce]

I would wonder if the variants are in a different order, can you just print all the lines to the snapshot to see what is different.

[famosab]

@SPPearce Changed it to assert the first 100 variants (which are more than are contained). Do you think thats ok?

[SPPearce]

Sure, its just to try and debug the issue

[famosab]

Now only the linting fails - so I am not sure why the md5sums are different on the runners and locally.

[SPPearce]

Ok, tests are passing!
It would be nice to gzip the output for space reasons, but I'm not going to argue that.

[famosab]

Lets get this merged then for now :) I will put in a request with the parabricks people to enable bgzip.