Dysgy==1.6.4

[poddarharsh15]

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!
• 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

[nvnieuwk]

Very good! Only one comment :)

[nvnieuwk]

Are the variants also unstable? You could test them using the nft-vcf plugin which is already enabled in this repository

[poddarharsh15]

Hi @nvnieuwk,
Thank you for your comments. I apologize, but I didn't fully understand what you meant by "unstable variants."

[nvnieuwk]

Sorry I wasn't clear I meant the variant lines in the VCF. Are they exactly the same if you rerun the tool or do they differ too? (Unstable files are usually caused by timestamps in the header)

[poddarharsh15]

The output generated from the nf-core/sarek pipeline is identical to the output produced by running the Dysgu pipeline independently. For reference, I have attached some example screenshots below to illustrate the similarities.
PS: I still need to do some changes in the modules of dysgu that I haven't made yet but in theory it is working fine for now.

[nvnieuwk]

Aha that command INFO line is probably the reason for the unstable md5sum. Can you test the variants MD5 instead? See here on how to do this: https://github.com/seppinho/nft-vcf?tab=readme-ov-file#variantsmd5

[poddarharsh15]

seems like I need to use

Aha that command INFO line is probably the reason for the unstable md5sum. Can you test the variants MD5 instead? See here on how to do this: https://github.com/seppinho/nft-vcf?tab=readme-ov-file#variantsmd5

hi @nvnieuwk sorry for silly question but by adding below command line in the nf-test.config will this work, please let me know.

config {
  plugins {
    load "[email protected]"
  }
}

something like this??

config {
    testsDir "."
    workDir ".nf-test"
    configFile "conf/test.config"
    profile "test"
    plugins {
      load "[email protected]"
  }
}

[nvnieuwk]

nft-vcf is already enabled in this repository so you shouldn't have to do this

[SPPearce]

It looks like this PR was implemented in #5928