workflow02-可视化展示snakemake流程

rule bwa_map:
    input:
        "data/genome.fa",
        "data/samples/{sample}.fastq"
    output:
        "mapped_reads/{sample}.bam"
    shell:
        "bwa mem {input} | samtools view -Sb - > {output}"

rule samtools_sort:
    input:
        "mapped_reads/{sample}.bam"
    output:
        "sorted_reads/{sample}.bam"
    shell:
        "samtools sort -T sorted_reads/{wildcards.sample} "
        "-O bam {input} > {output}"
  
rule samtools_index:
    input:
        "sorted_reads/{sample}.bam"
    output:
        "sorted_reads/{sample}.bam.bai"
    shell:
        "samtools index {input}"

mkdir -p data/samples
touch data/genome.fa data/samples/{A..D}.fastq

snakemake --dag sorted_reads/{A,B}.bam.bai

$ snakemake --dag sorted_reads/{A,B}.bam.bai
Building DAG of jobs...
digraph snakemake_dag {
    graph[bgcolor=white, margin=0];
    node[shape=box, style=rounded, fontname=sans,                 fontsize=10, penwidth=2];
    edge[penwidth=2, color=grey];
        0[label = "samtools_index", color = "0.44 0.6 0.85", style="rounded"];
        1[label = "samtools_sort", color = "0.22 0.6 0.85", style="rounded"];
        2[label = "bwa_map\nsample: A", color = "0.00 0.6 0.85", style="rounded"];
        3[label = "samtools_index", color = "0.44 0.6 0.85", style="rounded"];
        4[label = "samtools_sort", color = "0.22 0.6 0.85", style="rounded"];
        5[label = "bwa_map\nsample: B", color = "0.00 0.6 0.85", style="rounded"];
        1 -> 0
        2 -> 1
        4 -> 3
        5 -> 4
}

# conda install -y graphviz 
snakemake --dag sorted_reads/{A,B}.bam.bai | dot -Tpng > output/dag.png