update module: BWA/MEM

[piplus2]

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

BWA/MEM should be able to generate SAM files as it expects a task.ext.args2 --output-fmt sam.
In that case, we can skip samtools view as bwa mem already produces that format.