Hello,

I am trying to write a script to automate my RNAseq pipeline in a Bash shell on Ubuntu. Very simply, the beginning of my script (written in Vim) looks like this:

#!/bin/bash
set -e
set -u
set -o pipefail

#set variable for samples text file
sample_info=samples.txt

#set variable for fastq files
fq=($(cut -f 3 "$sample_info"))

for fastqc_file in ${fq[@]}
do
        fastqc $fastqc_file
done

and the error I receive is

Skipping '~/Documents/bash_practice/tutorial/UMH_R1a.fastq' which didn't exist, or couldn't be read

The samples.txt is a simple file with 3 tab separated columns containing name, read #, and file path:

UMH R1  ~/Documents/bash_practice/tutorial/UMH_R1a.fastq
UMH R2  ~/Documents/bash_practice/tutorial/UMH_R2a.fastq
UMN R1  ~/Documents/bash_practice/tutorial/UMN_R1a.fastq
UMN R2  ~/Documents/bash_practice/tutorial/UMN_R2a.fastq

I know there is no issue with the file or location because when I run:

fastqc ~/Documents/bash_practice/tutorial/UMH_R1a.fastq

on its own, everything runs fine. So I think the issue must be with how the script is accessing or trying to process my samples.txt file.

I am new to writing scripts, so the answer may be something trivial, and my apologies if it is very obvious.

Thank you in advance, B