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In the code below we pipe the output from wc -l (number of lines in the FASTQ file) to awk, which executes its body (the statements between the curly braces ( {  } ) for each line of input. Here the input is just one line, with one field – the line count. The awk body just divides the 1st input field ($1) by 4 and writes the result to standard output. (Read more about awk in Some Linux commands: awk)

# Setup (if needed)
export CORENGS=/work/projects/BioITeam/projects/courses/Core_NGS_Tools 
mkdir -p $SCRATCH/core_ngs/fastq_prep
cd $SCRATCH/core_ngs/fastq_prep
ln -sf $CORENGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -sf $CORENGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

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