python - 缺少snakemake中所有规则的输入文件

Question

我正在尝试构建一个用于生物合成基因杂波检测的snakemake管道，但正在努力解决错误:

Missing input files for rule all:
antismash-output/Unmap_09/Unmap_09.txt
antismash-output/Unmap_12/Unmap_12.txt
antismash-output/Unmap_18/Unmap_18.txt

等等更多文件。据我所知，snakefile 中的文件生成应该可以正常工作:

    workdir: config["path_to_files"]
wildcard_constraints:
    separator = config["separator"],
    extension = config["file_extension"],
    sample = config["samples"]

rule all:
    input:
        expand("antismash-output/{sample}/{sample}.txt", sample = config["samples"])

# merging the paired end reads (either fasta or fastq) as prodigal only takes single end reads
rule pear:
    input:
        forward = "{sample}{separator}1.{extension}",
        reverse = "{sample}{separator}2.{extension}"

    output:
        "merged_reads/{sample}.{extension}"

    conda:
        "~/miniconda3/envs/antismash"

    shell:
        "pear -f {input.forward} -r {input.reverse} -o {output} -t 21"

# If single end then move them to merged_reads directory
rule move:
    input:
        "{sample}.{extension}"

    output:
        "merged_reads/{sample}.{extension}"

    shell:
        "cp {path}/{sample}.{extension} {path}/merged_reads/"

# Setting the rule order on the 2 above rules which should be treated equally and only one run.
ruleorder: pear > move
# annotating the metagenome with prodigal#. Can be done inside antiSMASH but prefer to do it out
rule prodigal:
    input:
        "merged_reads/{sample}.{extension}"

    output:
        gbk_files = "annotated_reads/{sample}.gbk",
        protein_files = "protein_reads/{sample}.faa"

    conda:
        "~/miniconda3/envs/antismash"

    shell:
        "prodigal -i {input} -o {output.gbk_files} -a {output.protein_files} -p meta"

# running antiSMASH on the annotated metagenome
rule antiSMASH:
    input:
        "annotated_reads/{sample}.gbk"

    output:
        touch("antismash-output/{sample}/{sample}.txt")

    conda:
        "~/miniconda3/envs/antismash"

    shell:
        "antismash --knownclusterblast --subclusterblast --full-hmmer --smcog --outputfolder antismash-output/{wildcards.sample}/ {input}"

这是我的 config.yaml 文件的示例:

file_extension: fastq
path_to_files: /home/lamma/ABR/Each_reads
samples:
- Unmap_14
- Unmap_55
- Unmap_37
separator: _

我看不出蛇文件中哪里出了问题而产生了这样的错误。对于这个简单的问题抱歉，我是snakemake的新手。

Answer 1

问题是您设置的全局通配符约束错误:

wildcard_constraints:
    separator = config["separator"],
    extension = config["file_extension"],
    sample = '|'.join(config["samples"])  # <-- this should fix the problem

然后立即出现另一个问题，即extension 和seperator 通配符。 Snakemake 只能从其他文件名推断这些应该是什么，你不能通过通配符约束实际设置它们。我们可以使用 f-string 语法来填写值应该是什么:

rule pear:
    input:
        forward = f"{{sample}}{config['separator']}1.{{extension}}",
        reverse = f"{{sample}}{config['separator']}2.{{extension}}"
    ...

和:

rule prodigal:
    input:
        f"merged_reads/{{sample}}.{config['file_extension']}"
    ...

看看snakemake regex如果通配符约束让您感到困惑，如果您对 f"" 语法以及何时使用单 { 和何时使用 double 感到困惑，请查找有关 f 字符串的博客{{ 来逃避它们。

希望有帮助!