Example of a snakemake project
Download the repository from github
git clone https://github.com/Redmar-van-den-Berg/dedup-region.git
Install and activate the conda environment.
conda env create --file environment.yml
conda activate dedup-region
There are three levels where configuration options are set, in decreasing order of priority.
- Flags passed to snakemake using
--config
, or in the specified--configfile
. - Setting specified in the PEP project configuration, under the key
dedup-region
- The default settings for the pipeline, as specified in the
common.smk
file
The following settings are available for the pipeline.
Option | Type | Explanation |
---|---|---|
umi_trie | Required binary | Compiled version of umi-trie (the tests use a dummy version that is not suitable for real data |
gtf file | Required gtf file | http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz |
transcripts | List of transcripts | Must match the transcript_id from the gtf file |
You can run the tests that accompany this pipeline with the following commands
# Check if requirements are installed, and run linting on the Snakefile
pytest --kwd --tag sanity
# Test the pipeline settings in dry-run mode
pytest --kwd --tag dry-run
# Test the performance of the pipeline by running on the test data
pytest --kwd --tag integration
- For transcripts located on the mitochondrion, make sure that you rename the
entries in the GTF file to use
M
instead ofMT
as chromosome name. - If a transcript has no coverage before deduplication, the remaining coverage after deduplication will be shown as 0%. 0% in the `trasncripts/{transcript}_exons.html graph.