mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
e0d820f9f4
* feat: add snpeff * fix: linting * fix: tests * fix: add csv output * fix: add params information * fix: improve script * Update software/snpeff/environment.yml * Update software/snpeff/environment.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
22 lines
697 B
Docker
22 lines
697 B
Docker
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
|
|
|
|
# Add conda installation dir to PATH (instead of doing 'conda activate')
|
|
ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH
|
|
|
|
# Setup default ARG variables
|
|
ARG GENOME=GRCh38
|
|
ARG SNPEFF_CACHE_VERSION=99
|
|
|
|
# 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-5.0 > nf-core-snpeff-5.0.yml
|