ENH: Added option to run annotate_reads_card in parallel with parsl

[VinzentRisch]

• solves ENH: Add possibility to parallelise the annotate_reads_card action. #60

• Changes method annotate_reads_card to pipeline that can be run in parallel with parsl.

Set up an environment for linux on Euler

mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  qiime2 q2cli q2templates q2-types rgi tqdm

conda activate q2-amr

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
pip install git+https://github.com/qiime2/qiime2.git@7b0e435369ea9611e1354147a1051d1f31b9f66a

Run it locally

1. First, clone the repo and checkout the PR branch:

git clone https://github.com/bokulich-lab/q2-amr.git
cd q2-amr
git fetch origin pull/61/head:pr-61
git checkout pr-61
pip install -e .

2. Download test files
   PR-61.zip

card db
3. Set Up

• create a cache folder in your scratch directory on euler and replace the path at --use-cache in the sh file with your cache path.

qiime tools cache-create --cache path/to/cache

4. Test it out!

sbatch < reads_anno_parallel.sh

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.45%. Comparing base (75d4efa) to head (2dc3b78).
Report is 1 commits behind head on main.

❗ Current head 2dc3b78 differs from pull request most recent head 1bbc44c

Please upload reports for the commit 1bbc44c to get more accurate results.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #61      +/-   ##
==========================================
+ Coverage   94.29%   94.45%   +0.15%     
==========================================
  Files          20       20              
  Lines        1491     1534      +43     
==========================================
+ Hits         1406     1449      +43     
  Misses         85       85              

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[ChristosMatzoros]

Hey @VinzentRisch,

Everything works as expected in Euler, for the parallel execution of annotate_reads_card action. The code of the pipeline is also very clean and well structured. Please make the small correction in the description of card_db parameter. I think after that we are ready to merge this PR! 🚀