python - Snakemake 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，我想从包含 bob、clara 和 tim 的 vcf 文件中选择，只有在 roder 中的字典的第一个基因型（即 bob）作为第二条规则的输出bob.dn.vcf。这可能snakemake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

至少有两种选择：

1. 明确指定输出：

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

2. 对通配符值施加约束：

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

3. 通过为 rule 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"