fix a few tests after restructure

[rpetit3]

Related to https://github.com/nf-core/modules/issues/2154

Manually inspected the following using TMPDIR=~ nf-core modules test for Docker, Singularity and Conda.

• [x] amrfinderplus/run
• [x] amrfinderplus/update
• [x] ariba/run
• [x] busco
• [x] dragonflye
• [x] mobsuite/recon
• [x] panaroo/run
• [x] pirate
• [x] prokka
• [x] roary
• [x] shovill
• [x] sistr
• [x] snippy/core
• [x] snippy/run
• [x] tbprofiler/profile

Most seemed fine, the PR fixes a few that needed updating