ENH: add collate-annotations action

[Sann5]

What's new

• In order to speed up both eggnog-diamond-search one can partition the input and run several of these actions in parallel.
• Then one can proceed to annotate the output with the eggnog-annotate action still on the partitioned outputs in order to keep benefiting from parallelization.
• Once this annotation is complete it makes sense to collate all of the outputs together into the same artifact.
• This PR introduces an action that does exactly this. Takes a collection of Featuredata[NOG] artifacts and collates them into a single artifact.
• Closes ENH: action to join ortholog annotations artifacts (FeatureData[NOG]) #138

Set up an environment

# For linux: 
# export MY_OS="linux"
# For mac:
export MY_OS="osx" 
wget "https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-"$MY_OS"-conda.yml"
conda env create -n q2-shotgun --file qiime2-shotgun-2024.2-py38-osx-conda.yml
rm "qiime2-shotgun-2024.2-py38-"$MY_OS"-conda.yml""

Run it locally

1. Clone the repo and checkout the PR branch

# Remove q2-moshpit so you can install your local version.
conda activate q2-shotgun
pip remove q2-moshpit

# clone from GitHub
cd <clone_here>
git clone [email protected]:bokulich-lab/q2-moshpit.git
cd q2-moshpit
gh pr checkout 139
pip install -e .

2. Let's get you some data to play with:

cd <download here>
wget https://polybox.ethz.ch/index.php/s/IClpzSmbZ6EDEeW/download -O artifacts.zip
unzip artifacts.zip

3. Test it out!

qiime moshpit collate-annotations --i-ortholog-annotations artifacts --o-collated-annotations collated_annotations.qza --verbose

Running the tests

pytest -W ignore -vv --pyargs q2_moshpit

[misialq]

Looks good @Sann5, thanks! I'll merge this one 🙌