Create singularity images from conda environments

NorwegianVeterinaryInstitute / Talos

A shotgun metagenomic analysis pipeline using nextflow

BSD 3-Clause "New" or "Revised" License

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Create singularity images from conda environments #44

Open Thomieh73 opened 2 years ago

Thomieh73 commented 2 years ago

I used conda.yml files to create the conda environments from scratch . That causes all kinds of installation issues, when trying it myself. Much better to generate singularity images of the environments.

Thomieh73 commented 1 year ago

Installation of conda environments of

multiqc (solved)
microbecencus
kraken

proved to be very difficult. This needs to be solved soon.

Thomieh73 commented 1 year ago

Conda environments are in the latest version of nextflow not enabled by default.

To use conda environments use:

conda.enabled = true

origin: https://www.nextflow.io/docs/latest/conda.html#enabling-conda-environment