set "-o pipefail" for filter_subsample_sequences and mafft_one_chr

[tomkinsc]

Previously, if the commands along the way in the pipeline fail, the tasks succeed. This adds "-o pipefail" so errors lead to non-zero exits.
This change may be needed elsewhere; only adding to these two tasks for now.

[dpark01]

Wait, what was silently failing in the pipes?

This only appears to affect the one line in each task that has cat, xargs, and the actual command. In one of these cases, there's a defensive grep in there to get rid of blank lines (that sometimes exist and sometimes don't, depending on the WDL execution engine we're running on), and I learned the hard way a while ago that grep exits 1 if it never matches the pattern (so set -e is good, but -o pipefail shouldn't be used if there's a grep in the pipe that might reasonably never match a pattern).

[tomkinsc]

Great point about the grep calls. The augur filter command was silently failing (succeeding with no output) when provided with an empty metadata file as a result of macOS Docker not staging files correctly. Maybe I'll change this to exit if the input is empty? Or we could enable pipefail only for the augur filter call?

[dpark01]

yeah either way, let's see. Maybe we can break out the grep as a separate line wrapped in a set +o pipefail; grep... ; set -o pipefail, so that the augur and mafft invocations get the proper pipefail precautions.... Separate PR though.

There's probably other reasons augur filter might fail, so checking for empty metadata won't address all of them.