Make sure conda environment is used by default in SCimilarity image#1311
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allyhawkins merged 2 commits intoAlexsLemonade:mainfrom Aug 27, 2025
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allyhawkins
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jaclyn-taroni
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This is a fix to hopefully help with the issues I'm seeing in AlexsLemonade/OpenScPCA-nf#175 where the scripts are being run in the image container without using the conda environment when running in Nextflow. This adds the path to the conda environment to
PATHand tells the image to use the conda environment by default, even when not running interactively.I built the image locally and did a test run with
OpenScPCA-nfwhere I just printed out the Python version and made sure it could load theanndatamodule and it works so I think this should be good 🤞