A repository for trying some snakemake tutorials and tricks.

Najlabioinfo

Make sure that you are in conda environment with snakemake installed

• Ref[1]
• You can use snakemake docker image : ** https://hub.docker.com/r/najlabioinfo/basicsmk

docker pull najlabioinfo/basicsmk

Make sure that you are in the right place(outside of your workdir):

• git clone https://github.com/NajlaBioinfo/snaktuto.git
• cd snaktuto/snaktuto/

You can run it within 2 ways

• python snaktuto.py or
• Step by step : Ref[Execute]

You must configure your configs/configuser.yaml file:

• [project-name] : change your project name.
• [username] : change your username.
• [data-input] : change your path to able data access.
• [workdir] : make sure that your output dir is accessible and have enough space.

snakemake --use-conda -n

snakemake prj_tree mini_report fastqc multiqc clean_all --use-conda --core 2 --latency-wait 10

snakemake --use-conda --cluster qsub --jobs 100

snakemake --use-conda --drmaa --jobs 100

• https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html
• https://snakemake.readthedocs.io/en/stable/tutorial/short.html
• https://www.youtube.com/watch?v=hPrXcUUp70Y
• [data source] : https://github.com/snakemake/snakemake-tutorial-data/archive/v5.4.5.tar.gz