Analyzing Twist Targeted Methylation Sequencing Data Using the Twist Human Methylome Panel
This workflow follows: "Analyzing Twist Targeted Methylation Sequencing Data Using the Twist Human Methylome Panel" technote from TwistBioscience.
note: This action has already been done for you if you work at Gustave Roussy. See at the end of this section
- Install snakemake and snakedeploy with mamba package manager. Given that Mamba is installed, run:
mamba create -c conda-forge -c bioconda --name bigr_epicure_pipeline snakemake snakedeploy pandas
- Ensure your conda environment is activated in your bash terminal:
conda shell.bash activate bigr_epicure_pipeline
Alternatively, if you work at Gustave Roussy, you can use our shared environment:
conda activate /mnt/beegfs/pipelines/unofficial-snakemake-wrappers/shared_install/bigr_epicure_pipeline/
Given that Snakemake and Snakedeploy are installed and available (see Installation), the workflow can be deployed as follows.
- Go to your working directory:
cd path/to/my/project
- Deploy workflow:
snakedeploy deploy-workflow https://github.com/gustaveroussy/twist-target-methylation-sequencing . --tag 0.1.0
Snakedeploy will create two folders workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs. Later, when executing the workflow, Snakemake will automatically find the main Snakefile in the workflow subfolder.
- Consider to put the exact version of the pipeline and all modifications you might want perform under version control. e.g. by managing it via a (private) Github repository
See dedicated config/README.md file for dedicated explanations of all options and consequences.
note: This action has been made easier for you if you work at Gustave Roussy. See at the end of this section
Given that the workflow has been properly deployed and configured, it can be executed as follows.
For running the workflow while deploying any necessary software via conda (using the Mamba package manager by default), run Snakemake with
snakemake --cores all --use-conda
Alternatively, at Gustave Roussy:
snakemake --cores all --use-conda '/mnt/beegfs/pipelines/unofficial-snakemake-wrappers/profiles/slurm-web/'
Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.
For further options, e.g. for cluster and cloud execution, see the docs.