snakemake - Snakemake 5.5.4 中的 ImproperOutputException

Question

我是snakemake的新手，最近我遇到了一个新错误，该错误是我从最新版本的snakemake中得到的。这是我的蛇规则

rule fastqc_raw:
    input:
        expand(directory("{fastqc_dir}/{samples}_fastqc/"),fastqc_dir = FASTQC_DIR, samples = SAMPLES_wo_extension)

rule do_fastqc_raw:
    input:
        expand("{fastq_dir}/{{samples}}.fastq.gz", fastq_dir =  inputDir)
    output:
        expand(directory("{fastqc_dir}/{{samples}}_fastqc/"),fastqc_dir = FASTQC_DIR)
    log:
        expand("{fastqc_dir}/{{samples}}.log", fastqc_dir = FASTQC_DIR)
    threads:
        10
    message:
        "performing fastQC of the sample : {wildcards.samples}"
    shell:
        """mkdir -p {output} && fastqc -q -t {threads} --outdir {output} --contaminants /home/Contaminants/idot.txt {input} 2> {log}"""

我收到以下错误，当我使用低于 5.2.0 的 Snakemake 版本时，我没有收到该错误

ImproperOutputException in line 10 of /home/FASTQC.snakefile: Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule do_fastqc_raw:

Answer 1

我认为您的目录位于规则do_fastqc_raw中的错误位置。

这个:

output:
    expand(directory("{fastqc_dir}/{{samples}}_fastqc/"),fastqc_dir = FASTQC_DIR)

应该是:

output:
    directory(expand("{fastqc_dir}/{{samples}}_fastqc/", fastqc_dir = FASTQC_DIR))