Workflow

Workflow

Organization

• A subdirectory for each output of each rule (absent by default)
• A subdirectory "images" containing all the images of the tools (absent by default, you will have to copy it from "Tools")
• A subdirectory "rules" with all the rules used in the workflow (one file per rule).
• A file "configuration.yml" containing all the necessary configurations for Reprochackthon.wf.
• A Snakefile "ReproHackathon.wf" with the workflow.
• A README file

Resume

Setup

Singularity

You can check the read-me from Tools about Singularity installation.

Snakemake

Using Anaconda (didn't work for me)

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Using Python (Worked for me)

pip install snakemake

Using Bash (worked for me ...)

sudo apt install snakemake

Check Installation

singularity --version
snakemake -v  

Prepare Images

from the source of the git directory run

cd Tools
./images.sh
cp -r Tools/images Worflow/images

Execution

Once the 'environment setup' is done : From the Workflow directory :

snakemake --use-singularity -s $PWD/ReproHackathon.wf --configfile $PWD/configuration.yml -j 1 -k --printshellcmds