Umitools/dedup adding log and bug workaround

[anoronh4]

PR checklist

Closes issue #3504: Stages input bam and bai in a subfolder using stageAs, in order to prevent the inputs from matching the wildcard in the bam output channel.
Closes issue #3505: Added log file parameter and output channel, and updated all pytests to check for the log file output.

This PR was created to combine PRs #3506 and #3507, based on a suggestion that the two PRs should be combined for easier review. Those PRs are now closed.

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[anoronh4]

@nvnieuwk i have combined PRs #3506 and #3507, as you suggested. Hopefully we can get this moving soon?

[nvnieuwk]

Nice! This is perfect! Can you also quickly add a stub section before merging? :)