Snakemake is a powerful and flexible workflow management system that allows users to create and execute complex workflows in a reproducible and efficient manner. It is particularly useful for bioinformatics and computational biology applications, but can be applied to any field that requires the coordination of multiple tasks and the management of large amounts of data.
Below is an example of bwa mapping :
rule bwa_map:
input:
"data/genome.fa",
"data/samples/A.fastq"
output: "path/to/outputfile",
"mapped_reads/A.bam"
shell:
"bwa mem {input} | samtools view -Sb - > {output}"
The first step is to go to snakemake's website follow the best practice to start ===> Snakemake