nf-core_modules/modules/cellranger/mkfastq/Dockerfile

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# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
# Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2
LABEL authors="Regina Reynolds, Gisela Gabernet <gisela.gabernet@gmail.com>" \
description="Docker image containing bcl2fastq2 and Cell Ranger"
# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
# Install procps and clean apt cache
RUN apt-get update --allow-releaseinfo-change \
&& apt-get install -y \
cpio \
procps \
rpm2cpio \
unzip \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
CELLRANGER_VER=6.1.2
COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
# Install bcl2fastq2
RUN \
cd /tmp && \
unzip bcl2fastq2-$BCL2FASTQ2_VER.zip && \
mv *.rpm bcl2fastq2-$BCL2FASTQ2_VER.rpm && \
rpm2cpio ./bcl2fastq2-$BCL2FASTQ2_VER.rpm | cpio -idmv && \
export PATH=/tmp/usr/local/bin/:$PATH && \
ln -s /tmp/usr/local/bin/bcl2fastq /usr/bin/bcl2fastq && \
rm -rf bcl2fastq2-$BCL2FASTQ2_VER.*
# Install cellranger
RUN \
cd /opt && \
tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz