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Snakemake只传递输出到shell命令中的第一个路径

snakemake python

Nikita Vlasenko · 技术社区 · 6 年前

我试图将所有路径同时输入到一个变量中 python 编写脚本 snakemake

rule neo4j:
  input:
      script = 'python/neo4j.py',
      path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
      path_to_umap = 'results/umap/{sample}_umap.csv',
      path_to_mtx = 'data_files/normalized/{sample}.csv'
  output: 'results/neo4j/{sample}/cells.csv', 'results/neo4j/{sample}/genes.csv', 
      'results/neo4j/{sample}/cl_nodes.csv', 'results/neo4j/{sample}/cl_contains.csv',
      'results/neo4j/{sample}/cl_isin.csv', 'results/neo4j/{sample}/expr_by.csv',
      'results/neo4j/{sample}/expr_ess.csv'
  shell:
      "python {input.script} -path_to_cl {input.path_to_cl} -path_to_umap {input.path_to_umap} -path_to_mtx {input.path_to_mtx} -output {output}"

当我进入 output 中的参数脚本它只看到第一条路径: 'results/neo4j/{sample}/cells.csv' 输出 python

2 回复 | 直到 6 年前

bli 6 年前

neo4j.py 脚本不接受多个文件 -output 参数:shell命令可能以文件的完整列表结尾(检查 -p 选择 snakemake ),但脚本只考虑第一个。

如果确实是这样的话,一个可能更干净的方法是修改编写脚本,以便对每个输出文件使用一个参数。

然后按如下方式修改规则:

rule neo4j:
    input:
        script = 'python/neo4j.py',
        path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
        path_to_umap = 'results/umap/{sample}_umap.csv',
        path_to_mtx = 'data_files/normalized/{sample}.csv'
    output:
        cells = 'results/neo4j/{sample}/cells.csv',
        genes = 'results/neo4j/{sample}/genes.csv',
        nodes = 'results/neo4j/{sample}/cl_nodes.csv',
        contains = 'results/neo4j/{sample}/cl_contains.csv',
        isin = 'results/neo4j/{sample}/cl_isin.csv',
        by = 'results/neo4j/{sample}/expr_by.csv',
        ess = 'results/neo4j/{sample}/expr_ess.csv'
    shell:
        """
        python {input.script} \\
            --path_to_cl {input.path_to_cl} \\
            --path_to_umap {input.path_to_umap} \\
            --path_to_mtx {input.path_to_mtx} \\
            --cells {output.cells} \\
            --genes {output.genes} \\
            --nodes {output.nodes} \\
            --contains {output.contains} \\
            --isin {output.isin} \\
            --by {output.by} \\
            --ess {output.ess}
        """

编辑

rule neo4j:
    input:
        script = 'python/neo4j.py',
        path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
        path_to_umap = 'results/umap/{sample}_umap.csv',
        path_to_mtx = 'data_files/normalized/{sample}.csv'
    output:
        'results/neo4j/{sample}/cells.csv',
        'results/neo4j/{sample}/genes.csv',
        'results/neo4j/{sample}/cl_nodes.csv',
        'results/neo4j/{sample}/cl_contains.csv',
        'results/neo4j/{sample}/cl_isin.csv',
        'results/neo4j/{sample}/expr_by.csv',
        'results/neo4j/{sample}/expr_ess.csv'
    shell:
        """
        python {input.script} \\
            --path_to_cl {input.path_to_cl} \\
            --path_to_umap {input.path_to_umap} \\
            --path_to_mtx {input.path_to_mtx} \\
            --out_dir results/neo4j/{wildcards.sample}
        """

The Unfun Cat 6 年前

rule hello:
    output:
        "woot", "hoot"
    run:
        for f in output:
            print(f)
        print(output[1])