Learning how to use the snakemake pipelining language
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Learning how to use the snakemake pipelining language
A paper that compare the use of a variety of workflows:
Followed the tutorial in this page: https://slowkow.com/notes/snakemake-tutorial/. The only varoiation is that I had to install graphviz tool using:
conda install -c anaconda graphviz
to be able to visualize the workflow.
When done with the basic tutorial I need to master how I can use it for the accreditation work. This is the best place to begin: https://snakemake.bitbucket.io/snakemake-tutorial.html
Finally, I need to go through the carpentries tutorial .
I can also use the documentation as a reference material: https://snakemake.readthedocs.io/en/stable/
The plan
Get the pipeline working then I can use it for the analysis for varinat calling pipeline. This will make it very easy for us to reproduce the pipeline in the future.
Code Snippets
14 15 | shell: 'echo {input.genome} {input.r1} {input.r2} > {output}' |
22 23 24 25 26 | run: with open(output[0], 'w') as out: for i in input: sample = i.split('.')[0] for line in open(i): |
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