epi2me-labs/wf-single-cell

use of licensed conda channels

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trum994 commented

Ask away!

Our organization no longer has a license to Anaconda and its licensed "default" channel. Does this workflow and the containers used here utilize in any way licensed conda products?

cjw85 commented

Some of our workflow containers are indeed built using conda package managers to install software components. Conda environments are built using micromamba. Historically the channel order when building environments has been set as:

channels:
    - nanoporetech
    - conda-forge
    - bioconda
    - defaults

so it is unlikely that packages from defaults would be included, as there would almost always be an equivalent in conda-forge. Our build infrastructure no longer includes the defaults channel.

If you would like to check the environments for yourself you can run, for example, the following on any of the containers used by the workflow:

docker run ontresearch/wf-single-cell:sha0fcdf10929fbef2d426bb985e16b81153a88c6f4 bash -c "list-conda"

The container names and tags can be inspected from the nextflow.config file in the repository.