The changes here should reduce the amount of time of our tests from ~37 minutes to ~23 minutes. Once the end-to-end tests separated from the step tests, this will further reduce the amount of time taken. The summary of changes are:
Reduce size of medaka tests input and only run 2 options.
Reduce size of illumina end to end inputs by 75%.
Reduce the size of the ONT end to end inputs by 50%.
Convert the VADR tests to step tests
Convert the SNAP and tailedseq tests to step tests.
Other small changes I've made are:
using pigz instead of gunzip to unzip large krakendb (already installed as a dependency on trimgalore)
added --duration=0 to the tests, so it prints the length of each test
Other small changes I've made are: using pigz instead of gunzip to unzip large krakendb (already installed as a dependency on trimgalore) added --duration=0 to the tests, so it prints the length of each test