mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-25 20:08:17 +00:00
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
|
|
LABEL \
|
|
author="Maxime Garcia" \
|
|
description="VEP 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-vep-104.3/bin:$PATH
|
|
|
|
# Setup default ARG variables
|
|
ARG GENOME=GRCh38
|
|
ARG SPECIES=homo_sapiens
|
|
ARG VEP_VERSION=99
|
|
|
|
# Download Genome
|
|
RUN vep_install \
|
|
-a c \
|
|
-c .vep \
|
|
-s ${SPECIES} \
|
|
-y ${GENOME} \
|
|
--CACHE_VERSION ${VEP_VERSION} \
|
|
--CONVERT \
|
|
--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
|
|
|
|
# Dump the details of the installed packages to a file for posterity
|
|
RUN conda env export --name nf-core-vep-104.3 > nf-core-vep-104.3.yml
|