dysgu_updated

[poddarharsh15]

PR checklist

Closes #5784

• 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

[poddarharsh15]

@famosab I have updated main.nf and meta.yml files for dysgu module please have a look, Thanks :)

[famosab]

Looks god :) I added a few comments and questions. Next step is implementing the tests.

[famosab]

I added some suggestions to include also gzipped files and also emit the index to the gzipped vcf (I think that is best practise). Maybe you can apply those changes and also run prettier on the code so that the tests might run.

[poddarharsh15]

Great, thanks I will accept all the commits and run prettier asap :)

[poddarharsh15]

I added some suggestions to include also gzipped files and also emit the index to the gzipped vcf (I think that is best practise). Maybe you can apply those changes and also run prettier on the code so that the tests might run.

Hi @famosab I tried to run prettier tests on github but it's emitting several errors, do I need to install prettier --check on my workstation to solve the errors?

[famosab]

I added some suggestions to include also gzipped files and also emit the index to the gzipped vcf (I think that is best practise). Maybe you can apply those changes and also run prettier on the code so that the tests might run.

Hi @famosab I tried to run prettier tests on github but it's emitting several errors, do I need to install prettier --check on my workstation to solve the errors?

You will need to use prettier to format your code on your machine and then push the changes. Other approaches did not work for me for some reason:

conda install prettier

Once installed, you can run prettier manually:

prettier -w .

This will overwrite files with formatting fixes To just check without auto-fixing, use prettier -c .

[poddarharsh15]

I added some suggestions to include also gzipped files and also emit the index to the gzipped vcf (I think that is best practise). Maybe you can apply those changes and also run prettier on the code so that the tests might run.

Hi @famosab I tried to run prettier tests on github but it's emitting several errors, do I need to install prettier --check on my workstation to solve the errors?

You will need to use prettier to format your code on your machine and then push the changes. Other approaches did not work for me for some reason:

conda install prettier

Once installed, you can run prettier manually:

prettier -w .

This will overwrite files with formatting fixes To just check without auto-fixing, use prettier -c .

Okay, I will do that. One more concern: is it necessary to finish the main.nf.test before running prettier --check?
Thank you very much.

[famosab]

Update versions

[maxulysse]

I don't think you should delete this file

[SPPearce]

Why is this being deleted?

[maxulysse]

I made this comment too

[poddarharsh15]

I don't know why this was happening I didn't delete that file maybe I made some mistake

[poddarharsh15]

Why is this being deleted?

Should I add it again manually?

[SPPearce]

Should this file not be here?

[poddarharsh15]

Sorry I didn't understand why manta?

[famosab]

how did this file get in here :D just remove it from the PR I'd say

[SPPearce]

The tool takes cram files too, given your test, so maybe call this something more generic? Can't recall off the top of my head what we typically use to mean bam/cram.

[poddarharsh15]

checked main.nf of manta instead of input_bam here it's described just input
will this work?

input:
  
   tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
   tuple val(meta2), path(fasta)
   tuple val(meta3), path(fai)
   path(config)

[SPPearce]

input and index sounds fine.

[famosab]

change it and update in the meta accordingly

[famosab]

@poddarharsh15 maybe it makes sense to start another clean PR where no files are changed that should not be, you could just create a branch in your repo, implemented the changes we actually want and then open the PR

[poddarharsh15]

@poddarharsh15 maybe it makes sense to start another clean PR where no files are changed that should not be, you could just create a branch in your repo, implemented the changes we actually want and then open the PR

@famosab Sure, that makes sense. I'll create a new branch in my repo, implement the necessary changes, and then open a clean PR.[additionally, I will add run add call submodules], thanks for the update I will get back to you asap :)