GitLab

Full rewrite of the pipeline

Merge latest changes and testing into develop

Add github workflow testing

This reverts commit fb607603.

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.