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https://github.com/MillironX/nf-core_modules.git
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1b24005f07
* refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
28 lines
977 B
Docker
28 lines
977 B
Docker
# Dockerfile to create container with Cell Ranger v6.1.2
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# Push to nfcore/cellranger:<VER>
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FROM continuumio/miniconda3:4.8.2
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LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
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description="Docker image containing Cell Ranger"
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# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
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# Install procps and clean apt cache
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RUN apt-get update --allow-releaseinfo-change \
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&& apt-get install -y \
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cpio \
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procps \
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rpm2cpio \
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unzip \
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&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
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# Copy pre-downloaded cellranger file
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ENV CELLRANGER_VER=6.1.2
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COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
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# Install cellranger
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RUN \
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cd /opt && \
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tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
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export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
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ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
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rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz
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