MV 命令在 Snakemake 规则中不移动文件

Question

我是运行这条在第一个shell命令中调用的新规则tin.py。该文件写入当前目录，这很好。我想在创建它们时或之后将它们移动到一个名为 rnaseqc 的新文件夹中。但是，只有一部分是，其余的都是错误的。错误是 set -euo pipefail。我究竟做错了什么？是什么让它变得更好？

rule tin:
    """
    Quality-control step to infer RNA integrity at the transcript level.
    TINs (transcript integrity numbers) are calculated for all canoncial
    protein-coding transcripts. TIN is analogous to a computationally derived
    RIN value. From the docs: requires a sort and indexed bam file.
    @Input:
        Sorted, duplicate marked genomic BAM file (scatter)
    @Output:
        RSeQC logfiles containing transcript integrity number information
    """
    input:
        bam = rules.picard_dupes.output.bam,
        bai = rules.picard_dupes.output.index,
        control = rules.rseqc.output.Rdist
    output:
        out1 = 'rnaseqc/{sampleID}_marked_duplicates.tin.xls',
        out2 = 'rnaseqc/{sampleID}_marked_duplicates.summary.txt'
    params:
        ## Can I make more user friendly?
        bedref = 'PATH/transcripts.protein_coding_only.bed12',
        outdir = 'rnaseqc'
    run:
        ## Can I make more user friendly?
        shell('python PATH/.local/bin/tin.py -i {input.bam} -r {params.bedref}')
        # moves to rnaseqc directory
        shell('mv *.{txt,xls} {params.outdir}')
        # tried this also and getting index out of range error
        #shell('find . -maxdepth 1 -name "*txt" -or -name "*xls" -exec mv {} {params.outdir}')

Answer 1

我的猜测是运行同时使用此规则的多个版本存在问题。当 sample2 的作业移动它的所有文件时，一项作业在运行ning sample1 的中间！您可以更新您的移动命令以仅针对有问题的示例：

shell('mv {wildcards.sampleID}_marked_duplicates.* {params.outdir}')

并且通常在运行块中使用 shell 指令而不是 shell 命令更可取。

MV 命令在 Snakemake 规则中不移动文件

MV command isnt moving files in Snakemake Rule

python

linux

find

mv

snakemake