nf-core_modules/modules/snpeff/Dockerfile

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FROM nfcore/base:1.14
LABEL \
author="Maxime Garcia" \
description="snpEff image for nf-core pipelines" \
maintainer="maxime.garcia@scilifelab.se"
# Install the conda environment
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SNPEFF_CACHE_VERSION=99
ARG SNPEFF_TAG=99
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_TAG}/bin:$PATH
# Download Genome
RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml