Define the STAR output as bam file

[LKress]

The STAR output file has to be a BAM file and no SAM file.

[priesgo]

LGTM.

I wonder why this was not a problem before. I could only improve this by checking that the format is right in the output of integration tests.

[LKress]

@priesgo I will check this further.
In my previous PR I did not consider the changed file ending when running STAR with the default outSAMtype parameter. Thus BAM file format is now forced. In the integration test, the output filename remains the same, as the file is renamed in the STAR process.

[priesgo]

Yup, I understand. You could check that it's a valid BAM with samtools. You would need to install it in the CI environment though, but that should be a piece of cake.