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epi2me-labs / wf-amplicon

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Update nextflow.config #14

Closed charlenelawdes closed 3 months ago

charlenelawdes commented 3 months ago

Included an Apptainer profile

julibeg commented 3 months ago

Hi @charlenelawdes and thanks for contributing!

The profile section of the nextflow.config is the same across all EPI2ME workflows and we try to keep it as clean and minimal as possible. Also, when installing apptainer, a synonymous singularity command is still installed as well I think (at least that used to be the case). Therefore, I don't think we will add an extra profile for apptainer (we'd also have to add extra profiles for podman, charliecloud, etc.).

If you want to use a custom profile, we recommend putting it into a local config file and running nextflow with nextflow run ... -c my-local.config .... Alternatively, you can also add the profile to your $HOME/.nextflow/config if you want to use it regularly. This is also what I do, for example.