Move CI to GitHub Actions

[samuell]

Description

This PR moves the CI workflow configuration from the previous Travis CI one to GitHub actions, as suggested in #174

Some more details of changes done:

• The install script uses micromamba instead of conda if inside GitHub actions
• Some dependency specs were adjusted to make the installation go through
• A pointer to a folder ${CONDA_PREFIX}/testproject was changed to ${CONDA_PREFIX}/testdata instead, since the former does not exist in the repo.
• Two smaller bugs identified by flake8 was fixed, along with a typo

You can check the output of the converted code on the actions tab of this repo.

Primary function of PR

• [ ] Hotfix
• [ ] Patch
• [x] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME
• us
• _conda activate S_microSALT_
• _(SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json_
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

_Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• [ ] Code tested by @octocat
• [ ] Approved to run at Clinical-Genomics by @sylvinite

[samuell]

I haven't successfully tested the installation on Hasta Stage yet, since it seems to break on some unrelated things (can not find databases etc).

I might need to discuss with some of you on how to best test this on Hasta.