nf-core/tools API documentation

Automated documentation for nf-core/tools (1.13)

conda_dockerfile

`PipelineLint.conda_dockerfile()`

Checks the Dockerfile for use with Conda environments

Note

This test only runs if there is both an environment.yml and Dockerfile present in the pipeline root directory.

If a workflow has a conda environment.yml file, the Dockerfile should use this to create the docker image. These files are typically very short, just creating the conda environment inside the container.

This linting test checks for the following:

All of the following lines are present in the file (where PIPELINE is your pipeline name):

FROM nfcore/base:VERSION
COPY environment.yml /
RUN conda env create --quiet -f /environment.yml && conda clean -a
RUN conda env export --name PIPELINE > PIPELINE.yml
ENV PATH /opt/conda/envs/PIPELINE/bin:$PATH

That the FROM nfcore/base:VERSION is tagged to the most recent release of nf-core/tools
- The linting tool compares the tag against the currently installed version of tools.
- This line is not checked if running a development version of nf-core/tools.

Note

Additional lines and different metadata can be added to the Dockerfile without causing this lint test to fail.