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I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations by activating the miniconda , then store results in a separate file. fastq and then read second file, perform the same operations and save results in new 2nd file.fastq using the bash script and python script

#!/bin/bash

# directory of with mutiple fastq files#
FILES= " /home/folder/sample"

for f in $ FILES

do 
  conda activate FAST_qc    # actibvating the miniconda
  echo "Process the file $f
  mkdir "$f"                # making directory
  fastqc "$f"               # task to perform
done
bfontaine
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Luffy
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  • Maybe you could click [edit], select your code with the mouse and click `{}` in the Formatting Toolbar beside **Bold** and *Italic* to format it as code – Mark Setchell May 24 '23 at 07:42
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    What is your question? Also, there’s a typo in your script: it should be `$FILES`, not `$ FILES`. – bfontaine May 24 '23 at 08:07
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    Try to solve all the issues that shellcheck will throw at you, and the you can try stating a question. – Poshi May 24 '23 at 11:41

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