Several containers are used within the wgs pipeline. There is a "default" container used for many processes, and some more narrow containers used for specific pipelines. For processes which use other than the default, containers are specified in the processes.
To build a Singularity container, you run the following command.
sudo singularity build name_of_your_container.sif Singularity
To retain the environment variables from the user, add the -E flag to the sudo command.
sudo -E singularity build name_of_your_container.sif Singularity
The base container can be built by navigating into the container directory and running the following command:
sudo -E singularity build name_of_your_container.sif Singularity
The container can be directly downloaded from here.
madeline2 is installed separately. The Singularity recipe for building it is found here.
The VEP container is built from a publicly available docker container. Currently, the pipeline uses version 103.
singularity pull docker://ensemblorg/ensembl-vep:release_103
When running this container, additional reference files needs to be provided. These are outlined in the [[4.2 Inputs - Annotation files]] page.
The CADD container can be retrieved from the Galaxy Project.
Alternatively (if working at CMD in Lund), it can be clone from GitHub as such:
git clone https://github.com/Clinical-Genomics-Lund/CADD-container/tree/v1.6
In addition, reference files needs to be downloaded. Note that the file is really large - 200GB zipped. Use wget with the -c flag such to allow continuing the download if it is interrupted.
wget -c https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/annotationsGRCh38_v1.6.tar.gz
Make sure that the lines in the Singularity recipe matches to where you have saved the annotations folder, i.e. the path in the following line:
ln -sr /fs1/resources/ref/hg38/annotation_dbs/CADD_v1.6/data/annotations/GRCh38_v1.6 GRCh38_v1.6
Note: At the moment this container assumes that you have access to the /fs1/viktor/misc-scripts directory, i.e. you are running at the servers in Lund.
Finally you build the container:
sudo -E singularity build cadd_v1.6.sif Singularity
This container is used for CNV-calling. It can retrieved from a Docker container provided by Broad Institute.
singularity pull docker://broadinstitute/gatk
Normally, Sentieon containers are retrieved from the Galaxy Project
The container for the 2023 version seems not to work correctly (i.e. it crashes when running sentieon driver). An alternative container was be built from the Docker container found here for the 2023 version.
A Singularity recipe for Stranger is found here.
Alternatively, the Stranger container can be retrieved from the Galaxy Project.
Different versions of the twist-myeloid container are used for the cnv-kit and freebayes processes.
FIXME: While we still use this container, would we include the recipe?
A repository containing the recipe to build the AnnotSV container can be retrieved as such:
git clone https://github.com/Clinical-Genomics-Lund/annotsv_container.git
To build the container, cd into the repository and run the following command:
sudo singularity build annotsv.v2.3.sif Singularity
A POD container can be built using the recipe found here.
A Genmod container can be retrieved from the Galaxy Project.
A REViewer container can be built using the recipe found here.
A Melt container can be retrieved from the Galaxy Project.