This is the Snakemake workflow for VirusIntegrationFinder. The main configuration in the config.yaml file.
- Kimmo Palin (@kpalin)
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above).
- Create a new github repository using this workflow as a template.
- Clone the newly created repository to your local system, into the place where you want to perform the data analysis.
Configure the workflow according to your needs via editing config/config.yml file. The important
parts are INSERTED_SEQUENCE_FASTA containing the inserted viral sequence, INPUT_FASTQ containing
the long whole genome reads and GENOME_REFERENCE for getting genomic context and coordinates of
the insertions.
Install Snakemake using conda:
conda create -n vfind --file workflow/envs/myenv.yaml
For installation details, see the instructions in the Snakemake documentation.
Activate the conda environment:
conda activate vfind
Test your configuration by performing a dry-run via
snakemake -s workflow/Snakefile -n
Execute the workflow locally via
snakemake -s workflow/Snakefile--cores $N
using $N cores or run it in a cluster environment via
snakemake -s workflow/Snakefile --cluster qsub --jobs 100
or
snakemake -s workflow/Snakefile --drmaa --jobs 100
See the Snakemake documentation for further details.
After successful execution, you can create a self-contained interactive HTML report with all results via:
conda install jinja2 pygraphviz pygments
snakemake --report report.html
This report can, e.g., be forwarded to your collaborators. THIS IS NOT VERY USEFUL. JUST TECHNICAL RUNTIME ETC
Whenever you change something, don't forget to commit the changes back to your github copy of the repository:
git commit -a
git push