Merge master with IMPirisv2

Before starting to change/update the pipeline for the paper review, I would suggest to add the latest changes to the master branch.

The changes address some of the already existing issues.

changed milestone to %Paper review - Microbiome - 1

changed title from Im pirisv2 to Merge master with IMPirisv2

changed the description

added 8 commits

• ef37261f...fef0c395 - 7 commits from branch master
• 65e346d7 - Merge branch 'master' into 'IMPirisv2'

Compare with previous version

merged

mentioned in commit d80a6ad1