Add bcl2fastq2 to cellranger dockerfile (#1115)

* 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>
This commit is contained in:
Regina Hertfelder Reynolds 2022-01-25 18:58:22 +00:00 committed by GitHub
parent dcce431d51
commit 1b24005f07
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
13 changed files with 120 additions and 22 deletions

View file

@ -1 +1,2 @@
cellranger-*.tar.gz cellranger-*.tar.gz
bcl2fastq2-*.zip

View file

@ -1,15 +1,22 @@
# Dockerfile to create container with Cell Ranger v6.1.2
# Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2 FROM continuumio/miniconda3:4.8.2
LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \ LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
description="Docker image containing Cell Ranger" description="Docker image containing Cell Ranger"
# Disclaimer: this container is not provided nor supported by 10x Genomics. # Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
# Install procps and clean apt cache # Install procps and clean apt cache
RUN apt-get update --allow-releaseinfo-change \ RUN apt-get update --allow-releaseinfo-change \
&& apt-get install -y procps \ && apt-get install -y \
cpio \
procps \
rpm2cpio \
unzip \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/* && apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Copy pre-downloaded cellranger file # Copy pre-downloaded cellranger file
ENV CELLRANGER_VER 6.0.2 ENV CELLRANGER_VER=6.1.2
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
# Install cellranger # Install cellranger

View file

@ -1,18 +1,24 @@
# Updating the docker container and making a new module release # Updating the docker container and making a new module release
Cell Ranger is a commercial tool by 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger version in the container and pushing the update to Dockerhub needs to be done manually. Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the [Cell Ranger download page](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) and download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies. 1. Navigate to the appropriate download page.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile: update the Cell Ranger version in this line: 2. Edit the Dockerfile. Update the Cell Ranger versions in this line:
```bash ```bash
ENV CELLRANGER_VER <VERSION> ENV CELLRANGER_VER=<VERSION>
``` ```
3. Create the container: 3. Create and test the container:
```bash ```bash
docker build . -t nfcore/cellranger:<VERSION> docker build . -t nfcore/cellranger:<VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/cellranger:<VERSION> docker push nfcore/cellranger:<VERSION>
``` ```

View file

@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
} }
container "nfcore/cellranger:6.0.2" container "nfcore/cellranger:6.1.2"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

View file

@ -0,0 +1,40 @@
# 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

View file

@ -0,0 +1,26 @@
# Updating the docker container and making a new module release
Bcl2fastq2 and Cell Ranger are commercial tools from Illumina and 10X Genomics, respectively. The container provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating the bcl2fastq2 or Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download pages.
- [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:
```bash
ENV BCL2FASTQ2_VER=<VERSION> \
CELLRANGER_VER=<VERSION>
```
3. Create and test the container:
```bash
docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```

View file

@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
} }
container "litd/docker-cellranger:v6.1.1" // FIXME Add bcl2fastq to nf-core docker image container "nfcore/cellrangermkfastq:6.1.2"
input: input:
path bcl path bcl
@ -13,14 +13,14 @@ process CELLRANGER_MKFASTQ {
output: output:
path "versions.yml", emit: versions path "versions.yml", emit: versions
path "*.fastq.gz" , emit: fastq path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
""" """
cellranger mkfastq --id=${bcl.getSimpleName()} \ cellranger mkfastq --id=${bcl.getSimpleName()} \
--run=$bcl \ --run=$bcl \
--csv=$csv --csv=$csv \
$args $args
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
@ -28,4 +28,15 @@ process CELLRANGER_MKFASTQ {
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' ) cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS END_VERSIONS
""" """
stub:
"""
mkdir -p "${bcl.getSimpleName()}/outs/fastq_path/"
touch ${bcl.getSimpleName()}/outs/fastq_path/fake_file.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
} }

View file

@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
} }
container "nfcore/cellranger:6.0.2" container "nfcore/cellranger:6.1.2"
input: input:
path gtf path gtf

View file

@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
} }
container "nfcore/cellranger:6.0.2" container "nfcore/cellranger:6.1.2"
input: input:
path fasta path fasta

View file

@ -8,12 +8,12 @@
- path: output/cellranger/sample-123/outs/metrics_summary.csv - path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131 md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5 - path: output/cellranger/sample-123/outs/molecule_info.h5
md5sum: cf03b2b3ca776a1c37aa3518e91268ba md5sum: 0e56836ef0725f2ab05f56ca5a71e55b
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
md5sum: 15441da9cfceea0bb48c8b66b1b860df md5sum: 15441da9cfceea0bb48c8b66b1b860df
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
md5sum: 7c3d49c77016a09535aff61a027f750c md5sum: 7c3d49c77016a09535aff61a027f750c
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5 - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
md5sum: 40c8df814eb8723b7317b234dc8222e9 md5sum: cdad1cd7b215d7137cf92515e81a8525
- path: output/cellranger/sample-123/outs/web_summary.html - path: output/cellranger/sample-123/outs/web_summary.html

View file

@ -2,4 +2,8 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: CELLRANGER_MKFASTQ {
ext.args = "--tiles 1101"
}
} }

View file

@ -1,13 +1,16 @@
- name: cellranger mkfastq test_cellranger_mkfastq_simple - name: cellranger mkfastq test_cellranger_mkfastq_simple
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
tags: tags:
- cellranger - cellranger
- cellranger/mkfastq - cellranger/mkfastq
# files: files:
# - path: output/cellranger/genome.filtered.gtf - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
# md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: cellranger mkfastq test_cellranger_mkfastq_illumina - name: cellranger mkfastq test_cellranger_mkfastq_illumina
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
tags: tags:
- cellranger - cellranger
- cellranger/mkfastq - cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e

View file

@ -11,7 +11,7 @@
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: 6d9b5f409bfea95022bc25b9590e194e md5sum: 6d9b5f409bfea95022bc25b9590e194e
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: a4e2b9bbf016c55b0d4d7bc1fa53896f md5sum: 5d8d1669cd251433505f183e1c9ed6bc
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 22102926fadf5890e905ca71b2da3f35 md5sum: 22102926fadf5890e905ca71b2da3f35
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA - path: output/cellranger/homo_sapiens_chr22_reference/star/SA