This workflow performs CLIP peak calling using omniCLIP.
- Joël Simoneau (@simojoe)
This example workflow uses some previously published S. pombe datasets. The GEO identifiers of the datasets used are the following :
To run the snakemake workflow, we recommend to usage of a conda environment for the snakemake installation. conda will also be needed during the execution of the workflow. Make sure it is installed on your system.
The following creates the snakemake conda environment.
$ conda create --name smake -c conda-forge -c bioconda snakemake=5.20.1
To use the environment, activate it in the following way.
$ conda activate smake
Get a copy of this workflow by cloning and or downloading its latest release.
To run the workflow as is, use the following command in the main directory.
snakemake --use-conda --cores=$NB_CORES
Where $NB_CORES is replaced by the number of cores you want to dedicate to
this workflow execution.
This workflow is still under-development. To be added:
- Information about configuration.
- More flexibility for the type of data to analyze.
This workflow structure is based upon other released snakemake workflows found in the snakemake-workflows repository.