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set +o pipefail # only the exit code of the last pipe component is returned
cat joblist.txt | head -5000 | cut -f 2 | sort | uniq -c | sort -k1,1nr | head -1 | awk '{print $1}'
echo $?         # exit code will be 0

quotes matter

We've already seen that quoting variable evaluation preserves the caller's argument quoting (see Quoting subtleties). But more specifically, quoting preserves any special characters in the variable value's text (e.g. tab or linefeed characters).

Consider this case where a captured string contains tabs, as illustrated below.

• evaluating "$txt" inside of double quotes preserves the tabs
• evaluating $txt without double quotes converts each tab to a single space

Since we usually want to preserve tabs, we want to evaluate these variables inside double quotes.

txt=$( echo -e "aa\tbb\tcc" )
echo $txt    # tabs converted to spaces
echo "$txt"  # tabs preserved

Suppose we read a list of values from a file and want to use them in a for loop after capturing the values into a variable. Here we want to evaluate the variable without quotes; otherwise, the result includes the original linefeed characters instead of being a list of words that a for loop wants:

runs=$( grep 'SA1903.$' joblist.txt | cut -f 2 )
echo "$runs"   # preserves linefeeds
echo $runs     # linefeeds converted to spaces

for run in $runs; do
  echo "Run name is: $run"
done

reading file lines

The read function can be used to read input one line at a time. While the full details of read are complicated (see https://unix.stackexchange.com/questions/209123/understanding-ifs-read-r-line) this read-a-line-at-a-time idiom works nicely. 

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perl -p -e '~s/<search pattern>/<replacement<replacement>/;'

# for example:
cat joblist.txt | perl -ne 'print if $_ =~/SA18\d\d\d$/' | \
  perl -pe '~s/JA/job /' | perl -pe '~s/SA/run /'

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