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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
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LABEL \
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author="Maxime Garcia" \
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description="snpEff image for nf-core pipelines" \
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maintainer="maxime.garcia@scilifelab.se"
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# Install the conda environment
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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# Add conda installation dir to PATH (instead of doing 'conda activate')
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ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH
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# Setup default ARG variables
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ARG GENOME=GRCh38
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ARG SNPEFF_CACHE_VERSION=99
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# Download Genome
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RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
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# Dump the details of the installed packages to a file for posterity
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RUN conda env export --name nf-core-snpeff-5.0 > nf-core-snpeff-5.0.yml
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