Sigprofilerextractor

[pawelqs]

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

[pawelqs]

Hi @itrujnara ! I am sorry for not notifying you, but the PR was not yet ready, I just hoped that Github Actions will deploy the container when I open it, as I was advised by colleagues. I will fix it as soon as possible and ask you to review it again when its ready

[pawelqs]

Unfortunatelly I may not be able to complete this module in the nearest future. I will make a summary below in case that someone would like to take it over.

• SigProfilerExtractor does not take a reference genome as an input file, but takes a genome name and expects it to be installed by SigProfilerMatrixGenerator somewhere in the library directories, where it cannot be installed in Docker
• this genome installation is only required for the VCF input, not for matrix input. It should be possible then to implement sigprofiler/matrixgenerator module which would create the matrix files, which would be passed to sigprofiler/extractor module
• genome issue should not be relevant for sigprofiler/matrixgenerator module - this tool can be run in shell and this script can install genome to the working directory

#!/usr/bin/bash
mkdir -p tsb
SigProfilerMatrixGenerator install -v . ${genome}

• hopefully, SigProfilermatrixGenerator can use this genome to build the matrix file. SigProfilerExtractor cannot (or at least I was not able to make it running)
• Yes, everytime the process is run it will install the genome de novo. There is no way to install it once and pass the files

I may come back to this sooner or later, but feel free to contact me if you want to take it over earlier.

[famosab]

I will close the issue for now. If you get back to it feel free to reopen. If someone else picks this up they will still be able to find the PR :)