Adding extra options and increasing reproducibility

[tinytyranid]

We are currently implementing the susCovONT pipeline, during this we have noticed that for us some of the tools would not work together unless they all were a specific version. We also had some need for some extra options as our goal is to automate it and at the same time increase reproducibility while doing so.

These are the changes we have implemented:

• Version of tools that work together are specified in install.sh to make initial setup a bit easier
• The tag.json from Nextclade is now moved to retain the information of the Nextclade database/tag that was used (005_nextclade/nextclade-tag.json)
• We have added some extra options while running the pipeline:
  • -y, --yes for running the pipeline non-interactively and give an automatic yes to all prompts
  • --nextclade_ver for specifying the Nextclade version one would want to use
  • --nextclade_data_ver for specifying the Nextclade database tag that one would like to use
  • --keep_pangolin_ver for running the pipeline without updating Pangolin
  • -u, --user-id for specifying the user id for running docker commands
  • We have also updated the help text of some of the options that were already present
  • While adding these options we have made sure that the defaults are as they were from before, so a user that was running the pipeline before does not have to change the commands they are using now
• We have also done some small fixes that we have come across while implementing these changes

Thank you for the great work you have done on developing this pipeline!

Edit 03.11.2022

• Added Dockerfile
• Added a basic usage example using the Dockerimage
• Added actions/ci for the docker