MultiQC can run out of /tmp space on execution nodes on shark, leading
to incorrect results or crashes. This commit fixes this problem by
specifying a default location for the python tempfiles that MultiQC uses
via the environment variable TMPFILE inside of the shell block for the
MultiQC rule.

After renaming the pytest-workflow test cases, I forgot to update all
the marks for the tests of the stats output file, leading to some of
them always being skipped.

Picard HsMetrics requires both a file containing the targets of the
capture, as well as the actual baits used in the capture. However,
Agilent is refusing to share the baits of their older capture kits.

A common workaround for this issue is to simply specify the targets
file to picard twice.

This is supposed to speed up MarkDuplicates by up to 16%, see
https://github.com/broadinstitute/picard/issues/902 for details.

This reverts commit 1ad2f17f.

Since bwa-mem2 was removed from the pipeline, this workaround is no
longer needed.

This reverts commit 0cf92f4b.

bwa-mem2 can crash when multiple processes are running on the same
system. See https://github.com/bwa-mem2/bwa-mem2/issues/88 for details.

It appears this triggers some weird bug when used in combination with
bwa-mem2, which causes the alignment rule to crash randomly.

- Start every entry on a new indented line
- Make the order of the entries consistent in every rule
- Ensure equal signs are surrounded by spaces

Add test to make sure the markdup and baserecal groups receive the
correct inputs when a sample has multiple readgroups.