Keep the original source of the tumor cell content in the reports

[maehler]

In the current implementation of the CNV analysis, the html report that ends up in the results has the tumor cell content source specified as "pathology_purecn". If you don't know the criteria used for choosing one or the other this doesn't mean anything for someone reading the report. In my opinion it would be better to simply keep the original source in the report that ends up in the final results. As usual, both reports would be available under additional_files.

The file name could still have "pathology_purecn" in it to indicate that there was a choice made between the two, but in the metadata inside the report the original source should be listed. Is there anything preventing us from doing it like this? Right now the method is taken from the wildcards, but it would be pretty straightforward to write a function for getting the original method.

Related to this, would it be reasonable to to choose the purecn tumor content for the final report if there is no tumor cell content defined in the samples file? At the moment it is not possible to not specify tumor cell content in this pipeline, but the cnv_sv module now has support for missing values.