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https://github.com/MillironX/nf-core_modules.git
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7b4a28b6e8
* feat: add VEP module * fix: name * fix: EC lint] * feat: add info about params * fix: params as params, not input * fix: improve script * Update software/ensemblvep/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 * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
30 lines
836 B
Docker
30 lines
836 B
Docker
FROM nfcore/base:1.14
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LABEL \
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author="Maxime Garcia" \
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description="VEP 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-vep-104.3/bin:$PATH
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# Setup default ARG variables
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ARG GENOME=GRCh38
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ARG SPECIES=homo_sapiens
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ARG VEP_VERSION=99
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# Download Genome
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RUN vep_install \
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-a c \
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-c .vep \
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-s ${SPECIES} \
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-y ${GENOME} \
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--CACHE_VERSION ${VEP_VERSION} \
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--CONVERT \
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--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
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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-vep-104.3 > nf-core-vep-104.3.yml
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