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Snakemake is a workflow manager that enables massively parallel and reproducible analyses. Snakemake allows to build workflow by joing discrete steps, with each step having input and output files.
The Workflow
The
Snakefile
contains rules which define the output files we want to generate and how to build them.
Snakemake automatically builds a directed acyclic graph (DAG) of jobs to figure
out the dependencies of each of the rules and what order to run them in.
This workflow process the raw files quality control
fastqc and multiqc
, calls
bwa mem
to aligned reads to
the reference genome, calls
samtools sort
to sort the alinged reads, calls
picard.jar MarkDuplicates
to mark duplicate reads, calls
samtools index
to index sorted and marked duplicate reads, and finally calls
freebayes
to detect genetic variant and outputs a VCF file.
Tools need to run the pipeline
Code Snippets
23 24 | shell: "fastqc {input} -o {output} 2> {log}" |
33 34 | shell: "multiqc {input} --force -o {output} 2> {log}" |
45 46 47 | shell: "(bwa index {input.ref} " "&& bwa mem {input.ref} {input.r1} {input.r2} | samtools view -Sbh > {output}) 2> {log}" |
56 57 | shell: "samtools sort {input} -o {output} 2> {log}" |
67 68 69 | shell: "(java -jar /usr/local/Cellar/picard-tools/2.25.7/libexec/picard.jar MarkDuplicates INPUT={input} OUTPUT={output.dup} " "METRICS_FILE={output.met}) 2> {log}" |
78 79 | shell: "samtools index {input} 2> {log}" |
89 90 | shell: "freebayes -f {input.ref} {input.bam} > {output} 2> {log}" |
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