Snakemake 将 vcf 文件的第一个基因型作为输出中的通配符

Question

在第二条规则中，我想 select 从包含 bob、clara 和 tim 的 vcf 文件中，仅将 roder 中字典的第一个基因型（即 bob）作为第二条规则中的输出 bob.dn.vcf。这在 snakemake 中可行吗？

    d = {"FAM1": ["bob.bam", "clara.bam", "tim.bam"]}
    FAMILIES = list(d)
    
    rule all:
        input:
            expand some outputs
            
    wildcard_constraints:
        family = "|".join(FAMILIES)
    
    rule somerulename:
        input:
            lambda w: d[w.family]
        output:
            vcf="{family}/{family}.vcf"
        shell:
            """
            some python command line which produces a single vcf file with bob, clara and tim
            """
    
    rule somerulename:
        input:
            invcf="{family}/{family}.vcf"
        params:
            ref="someref.fasta"
        output:
            out="{family}/{bob}.dn.vcf"
        shell:
            """
            gatk --java-options "-Xms2G -Xmx2g -XX:ParallelGCThreads=2" SelectVariants -R {params.ref} -V {input.invcf} -O {output.out}
            """

Answer 1

至少有两个选项：

明确指定输出：

rule somerulename:
    output:
        out="FAM1/bob.dn.vcf"

对通配符值施加约束：

rule somerulename:
    output:
        out="{family}/{bob}.dn.vcf"
    wildcard_constraints:
        family="FAM1",
        bob="bob",

通过为规则指定适当的输入来控制生成的内容 all:

rule all:
    input: "FAM1/bob.dn.vcf", "FAM2/alice.dn.vcf"

Snakemake 将 vcf 文件的第一个基因型作为输出中的通配符

Snakemake first genotype of a vcf file as wildcard in output

python

snakemake

gatk