Samtools: replace rmdup by markdup

[bernt-matthias]

Description of feature

samtools rmdup has been deprecated and replaced by markdup. Would be awesome if this new tool would be supported in MultiQC.

[ewels]

Please attach one or more example outputs (zipped if necessary). Or better still, resubmit the issue using this issue template so that I have all of the info I need to write a new module. (Or better still, submit a PR 😉).

[ewels]

Note that I generally don't remove support for older tools / versions. I just try to support everything unless it becomes impossible for some reason.

[bernt-matthias]

Thanks for the feedback @ewels. I opened an issue here #1862

Note that I generally don't remove support for older tools / versions.

That's excellent.

[ewels]

Thanks!