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

[SPPearce]

Requires some tests before it can be merged.

[famosab]

You'll probably need to add another module (draft here: #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.

[SPPearce]

A few comments.

• The prefix can't have def before it if it is being used to define the output channels, as that makes it a local variable. Think that'll help with your tests.

• Requirements for the environment.yml have changed, so I've updated that.

• We are moving away from external links, even to other GitHub repositories, so it'd be good to use data in test datasets please

[SPPearce]

Suggested change

	def prefix = task.ext.prefix ?: "${meta.id}"
	prefix = task.ext.prefix ?: "${meta.id}"

[famosab]

Just because I am curious: I always see it the other way around (so that you need two times def and otherwise you run into errors). Has this changed? Is there any part of the docs you can point me to?

[bounlu]

Me too, I simply copy pasted it from other modules indeed.

[SPPearce]

Suggested change

	def prefix = task.ext.prefix ?: "${meta.id}"
	prefix = task.ext.prefix ?: "${meta.id}"

[SPPearce]

These look like folders not files

[bounlu]

They are files indeed.

[SPPearce]

Ok, then the stub needs to touch the files not mkdir them.

[SPPearce]

This looks completely empty? Probably because of the prefix issue

[SPPearce]

Suggested change

name: msisensorpro_msitumoronly

[SPPearce]

Suggested change

- defaults