在文件夹上使用类似名称的fastq文件，并将它们输入到脚本中(对对)

Question

我在一个文件夹中有一组文件名如下：

AM11_BW415_R1.fastq.gz         NAM13_BW968_R2.fastq.gz     NAM17_AC_Barrie_R1.fastq.gz  NAM3_PI648600_R2.fastq.gz  NAM7_Glenlea_R1.fastq.gz   PI648598_R2.fastq.gz
NAM11_BW415_R2.fastq.gz         NAM13_Frontana_R1.fastq.gz  NAM17_AC_Barrie_R2.fastq.gz  NAM3_PI648842_R1.fastq.gz  NAM7_Glenlea_R2.fastq.gz   PI648611_R1.fastq.gz
NAM11_Reeder_R1.fastq.gz        NAM13_Frontana_R2.fastq.gz  NAM17_BW388_R1.fastq.gz      NAM3_PI648842_R2.fastq.gz  NAM7_Laura_R1.fastq.gz     PI648611_R2.fastq.gz
NAM11_Reeder_R2.fastq.gz        NAM14_BW874_R1.fastq.gz     NAM17_BW388_R2.fastq.gz      NAM4_PI613279_R1.fastq.gz  NAM7_Laura_R2.fastq.gz     PI648672_R1.fastq.gz
NAM11_Webill_R1.fastq.gz        NAM14_BW874_R2.fastq.gz     NAM17_RedFife_R1.fastq.gz    NAM4_PI613279_R2.fastq.gz  NAM7_Marquis_R1.fastq.gz   PI648672_R2.fastq.gz
NAM11_Webill_R2.fastq.gz        NAM14_Glenn_R1.fastq.gz     NAM17_RedFife_R2.fastq.gz    NAM4_PI613280_R1.fastq.gz  NAM7_Marquis_R2.fastq.gz   PI648724_R1.fastq.gz
NAM12_BW431_L002_R1.fastq.gz    NAM14_Glenn_R2.fastq.gz     NAM1_PI648517_R1.fastq.gz    NAM4_PI613280_R2.fastq.gz  NAM8_FL62R1_R1.fastq.gz    PI648724_R2.fastq.gz
NAM12_BW431_L002_R2.fastq.gz    NAM14_Unity_R1.fastq.gz     NAM1_PI648517_R2.fastq.gz    NAM4_PI648524_R1.fastq.gz  NAM8_FL62R1_R2.fastq.gz    PI648768_R1.fastq.gz
NAM12_BW431_L008_R1.fastq.gz    NAM14_Unity_R2.fastq.gz     NAM1_PI648519_R1.fastq.gz    NAM4_PI648524_R2.fastq.gz  NAM8_Muchmore_R1.fastq.gz  PI648768_R2.fastq.gz
NAM12_BW431_L008_R2.fastq.gz    NAM15_BW881_R1.fastq.gz     NAM1_PI648519_R2.fastq.gz    NAM5_PI648523_R1.fastq.gz  NAM8_Muchmore_R2.fastq.gz  PI648860_R1.fastq.gz
NAM12_Penhold_L002_R1.fastq.gz  NAM15_BW881_R2.fastq.gz     NAM1_PI648541_R1.fastq.gz    NAM5_PI648523_R2.fastq.gz  NAM8_Stettler_R1.fastq.gz  PI648860_R2.fastq.gz
NAM12_Penhold_L002_R2.fastq.gz  NAM15_Lillian_R1.fastq.gz   NAM1_PI648541_R2.fastq.gz    NAM5_PI648585_R1.fastq.gz  NAM8_Stettler_R2.fastq.gz  PI648862_R1.fastq.gz
NAM12_Penhold_L008_R1.fastq.gz  NAM15_Lillian_R2.fastq.gz   NAM2_PI648493_R1.fastq.gz    NAM5_PI648585_R2.fastq.gz  PI277012_R1.fastq.gz       PI648862_R2.fastq.gz
NAM12_Penhold_L008_R2.fastq.gz  NAM15_PT245_R1.fastq.gz     NAM2_PI648493_R2.fastq.gz    NAM5_PI648622_R1.fastq.gz  PI277012_R2.fastq.gz       PI648864_R1.fastq.gz
NAM12_Sumai3_L002_R1.fastq.gz   NAM15_PT245_R2.fastq.gz     NAM2_PI648602_R1.fastq.gz    NAM5_PI648622_R2.fastq.gz  PI648478_R1.fastq.gz       PI648864_R2.fastq.gz
NAM12_Sumai3_L002_R2.fastq.gz   NAM16_BA51B92_R1.fastq.gz   NAM2_PI648602_R2.fastq.gz    NAM6_Neepawa_R1.fastq.gz   PI648478_R2.fastq.gz       run_701_150904_7001410_0194_BC79VNANXX_NAM.list
NAM12_Sumai3_L008_R1.fastq.gz   NAM16_BA51B92_R2.fastq.gz   NAM2_PI648609_R1.fastq.gz    NAM6_Neepawa_R2.fastq.gz   PI648487_R1.fastq.gz       run_760_160912_7001343F_0065_AC9EV0ANXX_NAM.list
NAM12_Sumai3_L008_R2.fastq.gz   NAM16_BW928_R1.fastq.gz     NAM2_PI648609_R2.fastq.gz    NAM6_PI648532_R1.fastq.gz  PI648487_R2.fastq.gz
NAM13_BW462_R1.fastq.gz         NAM16_BW928_R2.fastq.gz     NAM3_PI648511_R1.fastq.gz    NAM6_PI648532_R2.fastq.gz  PI648566_R1.fastq.gz
NAM13_BW462_R2.fastq.gz         NAM16_BW963_R1.fastq.gz     NAM3_PI648511_R2.fastq.gz    NAM6_Thatcher_R1.fastq.gz  PI648566_R2.fastq.gz
NAM13_BW968_R1.fastq.gz         NAM16_BW963_R2.fastq.gz     NAM3_PI648600_R1.fastq.gz    NAM6_Thatcher_R2.fastq.gz  PI648598_R1.fastq.gz

因此，我想为循环或单个for循环做一些工作，这些循环能够接受两个类似名称的文件，例如NAM11_Reeder_R1.fastq.gz，然后以以下方式将它们作为该文件夹之外的脚本的参数：

 scripts/PipelineHaplo.sh raw/NAM13_BW968_R1.fastq.gz raw/NAM13_BW968_R2.fastq.gz 2 &

这2指定了读取的深度，但为了简单起见，让我们说，这是一个不变的、不同的论点，我几乎可以硬编码。

然后，我希望它获取接下来的两个参数(原始文件)、R1和R2，并进行同样的操作。那么，如果让脚本在不正确的文件夹上应用论述，我又如何做到这一点。基本上，所有这些都在主文件夹中，其中的文件夹是:原始文件、脚本--一大组基本上是空的目录，名为cases{001.008}，上面有子目录

这就是我希望脚本工作的地方，所以脚本首先首先要将R1和R2移动到一个名为raw和raw的文件夹中，下一个脚本就在那里控制它并完成它的工作。

这个循环只取两个相同名称的文件，它会是什么样的呢？

Answer 1

与GNU并行，如下所示：

parallel scripts/PipelineHaplo.sh {} '{=s/_R1/_R2/=}' 2 ::: raw/*R1.fastq.gz