Added new module: msisensorpro/msitumoronly

[bounlu]

This module enables tumor-only analysis for msisenspro (msisensor-pro pro)

[SPPearce]

Can you please add some tests via nf-core modules test msisensorpro/msitumoronly

[famosab]

You'll probably need to add another module (draft here: https://github.com/nf-core/modules/pull/6536) to create the baseline. Or you have to add a baseline file to the test-datasets for the tests to run. Afaik the scan is not enough to run msitumoronly afterwards.

[bounlu]

As a default baseline for hg38, this file can be added.

[famosab]

I tried with your baseline and the test data from their repo and always got this error:

│     Program aborted:                                                                                                                                                                                                                                                │
│     Same reference genome file should be used in both scan and msi/pro/baseline steps!!!

Maybe you can find the correct files that should be used here.

[famosab]

The stub is also not working as expected:

│   Caused by:                                                                                                                                                                                                                                                        │
│     Missing output file(s) `null` expected by process `MSISENSORPRO_MSITUMORONLY (test)`                                                                                                                                                                            │
│                                                                                                                                                                                                                                                                     │
│                                                                                                                                                                                                                                                                     │
│   Command executed:                                                                                                                                                                                                                                                 │
│                                                                                                                                                                                                                                                                     │
│     mkdir test                                                                                                                                                                                                                                                      │
│     mkdir test_dis                                                                                                                                                                                                                                                  │
│     mkdir test_all                                                                                                                                                                                                                                                  │
│     mkdir test_unstable                                                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                                                     │
│     cat <<-END_VERSIONS > versions.yml                                                                                                                                                                                                                              │
│     "MSISENSORPRO_MSITUMORONLY":                                                                                                                                                                                                                                    │
│         msisensor-pro: $(msisensor-pro 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p')                                                                                                                                                                          │
│     END_VERSIONS    

[bounlu]

I tried with your baseline and the test data from their repo and always got this error:

│     Program aborted:                                                                                                                                                                                                                                                │
│     Same reference genome file should be used in both scan and msi/pro/baseline steps!!!

Maybe you can find the correct files that should be used here.

Hi. Thanks for testing. This error is not related to the pipeline, but to msisensorpro. It seems you are using a bam file incompatible with the chromosome names in the baseline. It works for me if I choose the default GRCh38 in sarek.

Not sure about the stub failure as I haven't added it.

[famosab]

Bump @bounlu :)

[luisas]

Hi @bounlu any plans to work on this one? :)

We are doing some nf-core cleaning and we are planning to close, by the end of this week, PRs that nobody works on anymore. They can be then ofc reopened in the future in case it is needed.

[github-actions[bot]]

This PR has been tagged as awaiting-changes or awaiting-feedback by an @nf-core/modules contributor. Remove stale label or add a comment if it is still useful.

[famosab]

Closing due to inactivity - feel free to open a fresh PR