centralising container links and integrate mutscan for fitness calculation

[BenjaminWehnert1008]

…ation

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/deepmutscan branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[BenjaminWehnert1008]

@MaximilianStammnitz please check on the changes I've made in the mutscan R script

And I'm not sure if we need this Readme. At least we don't have it in other modules

[BenjaminWehnert1008]

@MaximilianStammnitz I have decentralized the container links again, because many tests were failing...

[BenjaminWehnert1008]

@mashehu, can you help us with the test that is still failing? Not quite sure what's going on there. Maybe it's related to the snapshot?

[mashehu]

FYI: this is the docker container for singularity please use the https link as described here: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers

[BenjaminWehnert1008]

thanks, this is very valuable feedback! :)

[mashehu]

How did you generate the snapshots? Because you updated the containers that usually means the snapshot also changes. Try to regenerate them with the last changes.

[BenjaminWehnert1008]

@mashehu The snapshot still seems to be not 100% equal. This is how I created the new snapshot after all changes:
nf-test test tests/default.nf.test --profile docker --update-snapshot
I'm working on a M1 Mac, may this be a problem?

[MaximilianStammnitz]

@MaximilianStammnitz please check on the changes I've made in the mutscan R script

And I'm not sure if we need this Readme. At least we don't have it in other modules

Yep, good to remove: #43

[MaximilianStammnitz]

would be great if you can also export and re-add the high-res pipeline.png, just so it is properly displayed in the main nf-core intro/readme (not sure why Github doesn't really allow for PDF image embeddings)

[MaximilianStammnitz]

looks awesome – only need to flip colours between pink & orange in the legend

[BenjaminWehnert1008]

damn it, sure!

[MaximilianStammnitz]

@BenjaminWehnert1008 do you think this is good to merge? or should we first fix the remainder issue via nf-test?

[mashehu]

@mashehu The snapshot still seems to be not 100% equal. This is how I created the new snapshot after all changes: nf-test test tests/default.nf.test --profile docker --update-snapshot I'm working on a M1 Mac, may this be a problem?

Could be, but there seems to be more going on, because you don't just have sha-sum missmatches, but multiqc produces more files in the CI it seems like. Can you try to run the tests in a github codespace?

[BenjaminWehnert1008]

Hey @mashehu,
thanks for the suggestions. I tried generating the snapshot in a Codespaces, but I keep running into environment limits:

Using --profile docker:
docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: unable to apply cgroup configuration: cannot enter cgroupv2 "/sys/fs/cgroup/docker" with domain controllers -- it is in an invalid state: unknown.

Using --profile conda:
The pipeline progresses well but eventually hits disk space limits (no space left on device), also after removing all environments/work directory etc before starting. This may be due to large packages llike GATK.