Use @ADDMEMORY@ / @ADDTHREADS@ macros appropriately across samtools c…

[wm75]

…ollection

Continuation of #3375

Fixes https://help.galaxyproject.org/t/samtools-fixmate-memory-allocation-error/17656

[wm75]

For the record:
there are more tools outside the samtools collection of tools that could benefit from using those TOKENS, too.

The tool that stands out as requiring fixing is arriba, which hard-codes memory usage of samtools sort thread, but determines threads from GALAXY_SLOTS.

[wm75]

Please note that here the change improves things, but the entire pipe using multiple threads at each step seems questionable.
@bernt-matthias maybe you have an idea how to fix this properly?

[bernt-matthias]

Are ampliconclip, collate and fixmate compute intense tasks that need a lot of memory / CPUs?

Maybe just remove the calls of collate, fixmate and sort completelty. It's not documented that these tools run anyway. If we would want to fix all problems that are potentially introduced by ampliconclip the docs suggest that we also should call calmd`... Let the user do this?

[wm75]

Unfortunately, I still have never used the tool.
I agree with your points, but then lets do this separately. I will try to understand what's required next week and then open a new PR with those changes.

[wm75]

added the skip-version-check label just for samtools sort with the cosmetic indentation change. All other changed tools should have version bumps now.