Didn't test but this should work:

awk '{print "touch "$1".fastq && cat "$2".fastq >> "$1".fastq"}' table.txt > runscript.sh
source runscript.sh

First generate a script of cat operations (look at it to see that it's valid!) and then run all the cats.

using nextflow

usage:

nextflow run --input config.tsv --basedir ${PWD} biostar375624.nf

Given this list was called foo.txt you can use:

cut -f1 foo.txt | \
  sort -k1,1 -u | \
  while read p; do 
    grep "${p}" foo.txt | \
    awk '{print $2".fastq"}' | \
    xargs cat > ${p}.fastq
    done < /dev/stdin

It first extracts the unique sample names, then loop-wise collects the names of the replicates that belong to one sample and then uses xargs together with cat to concatenate them.