fastqc not installed inside the container

[gmurtaza404]

Hello!

Thank you for sharing and maintain the pipeline! Really appreciate it!

I ran into an issue, where I can't run the run-fastqc.sh whether from inside (shell access) or outside (execute) the apptainer. To debug it further I found out that the 'fastqc' utility is not installed inside the container.

The run-fastqc.sh script internally calls the fastqc:

Apptainer> cat /usr/local/bin/run-fastqc.sh
#!/bin/bash

inputfile=$1
nthread=$2
outdir=$3

mkdir -p $outdir

if [[ $inputfile =~ \.gz$ ]]
then
  cp $inputfile $outdir/data.fastq.gz
  fastqc -t $nthread $outdir/data.fastq.gz
else
  cp $inputfile $outdir/data.fastq
  fastqc -t $nthread $outdir/data.fastq
fi

And when I try to check where is it, I get this error.

Apptainer> fastqc --version
bash: fastqc: command not found
Apptainer> whereis fastqc
fastqc:

Thank you!