bioinformatics - 影子规则上的 Snakemake 错误

Question

我尝试在此规则上使用影子规则。如果我评论阴影行没有没有错误。

rule Strelka_run:
    input:
         "mapped_reads/merged_samples{case}.sorted.dup.reca.bam",
         "mapped_reads/merged_samples{case}.sorted.dup.reca.bam",
         "Results/manta/{case}/results/variants/candidateSmallIndels.vcf.gz",
    shadow: "shallow"
    output:
        "Results/strelka/{case}/",
        "Results/strelka/{case}/results/variants/somatic.snvs.vcf.gz"
    params:
        genome=config['reference']['genome_fasta'],
        target= config['bed_target']['custom']
    log:
        "log/logss.strelka.txt"
    conda:
        "envs/strelka.yaml"
    shell:
         """
           configureStrelkaSomaticWorkflow.py --normalBam {input[1]} --tumorBam {input[0]} --referenceFasta   {params.genome} --indelCandidates {input[2]} --runDir {output[0]} --exome  && {output[0]}/runWorkflow.py -m local

         """

我有这个错误

RuleException in line 4 of rules/strelka.rules:
Could not resolve wildcards in rule Strelka_run:
case

标签： bioinformaticssnakemake