Snakemake问题：将所有文件与空格分隔符合并在一起，而不是通过它进行迭代]]

Question

我试图运行理想情况下看起来像这样的命令，

minimap2 -a -x map-ont -t 20 /staging/reference.fasta fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample01.bam

类似地，我在文件夹中有多个样本（指的是fastq / sample01.fastq

）。

但是，我为使这种行为自动化而编写的snakemake文件是在命令中同时解析所有文件，例如，

minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam

我已经在下面粘贴了代码和日志。请帮助我尝试找出此错误。

代码

SAMPLES, = glob_wildcards("fastq/{smp}.fastq")
rule minimap:
    input:
        expand("fastq/{smp}.fastq", smp=SAMPLES)
    output:
        expand("fastq_minon/{smp}.bam", smp=SAMPLES)
    params:
        ref = FASTA
    threads: 40
    shell:
        """
        minimap2 -a -x map-ont -t {threads} {params.ref} {input} | samtools view -bS -F 4 - | samtools sort -o {output}
        """
log

Building DAG of jobs...
Job counts:
        count   jobs
        1       minimap
        1

[Tue May  5 03:28:50 2020]
rule minimap:
    input: fastq/sample02.fastq, fastq/sample03.fastq, fastq/sample01.fastq
    output: fastq_minon/sample02.bam, fastq_minon/sample03.bam, fastq_minon/sample01.bam
    jobid: 0


        minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam

Job counts:
        count   jobs
        1       minimap
        1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

我正在尝试运行理想的命令，如下所示：minimap2 -a -x map-ont -t 20 /staging/reference.fasta fastq / sample01.fastq | samtools视图-bS -F 4-| samtools排序-o fastq_minon / ...

Answer 1

expand功能用于创建列表。因此，在您的规则minimap中，您告诉snakemake您希望所有fastq文件都作为输入，并且该规则将产生尽可能多的bam文件。您想要的是一个将使用通配符为每个样本触发的规则：