bash 中使用工具的嵌套循环

Question

我有一个正在尝试构建的循环。那是从不同的路径中提取文件。我需要将它们循环在一起。这是我拥有的：

#!/bin/bash
#SBATCH --mem=110g
#SBATCH --cpus-per-task=12

module load java/17.0.2

for bam in /PATH1/*.sorted.dmark.bam;
do
  java -Xmx110g -jar /PATHtoTOOL/fgbio-2.0.0.jar AnnotateBamWithUmis \
     -i bam \
     -f /PATH2/*_L001_UMI.fastq.gz \ # This is where I need the secodary loop
     -o bam.UMI.bam
done

Answer 1

用文件填充两个数组，按索引遍历它们：

#! /bin/bash
dmarks=(/PATH1/*.sorted.dmark.bam)
fastqs=(/PATH2/*_L001_UMI.fastq.gz)

if (( ${#dmarks[@]} != ${#fastqs[@]} )) ; then
    echo Different number of files >&2
    exit 1
fi

for (( i=0; i<${#dmarks[@]}; ++i)) ; do
    dmark=${dmarks[i]}
    fastq=${fastqs[i]}
    java -Xmx110g -jar /PATHtoTOOL/fgbio-2.0.0.jar AnnotateBamWithUmis \
        -i "$dmark" \
        -f "$fastq" \
        -o bam.UMI.bam
done

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