Correct error-detection for all Perl scripts

[vinjana]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

I/O operations like open or <> are not automatically checked for errors in Perl (compare Python, where exceptions are thrown). Instead for instance the <FH> operator returns undef if the file's end is reached or if there is an error on the stream (e.g. broken pipe).

Consequently, all usages of such function/operators in Perl need to explicitly guarded to ensure no I/O error happened.

This error can result in undetected partial processing of inputs files, in particular in less stable runtime environments and with a probability approach one when scaling out.

In the code it seems open is usually guarded (or die), but the <FH> operator is almost never guarded. Also read or write operations need to be guarded and possibly (unsure) also print FH ... should be guarded.

An example of correct(er) error handling:

my $line = readline(STDIN)
   || die "Couldn't read header from standard input: $!";

while (! eof(STDIN)) {
   my $line = readline(STDIN);
   if (! defined $line) {
     die "Couldn't read from standard input: $!";
   }
   doSomethingWith($line);
}

Command used and terminal output

None. Problem occurs sporadically.

Relevant files

Probably all Perl scripts lib/*.pl. All should be checked.

System information

This is valid for all versions of Perl and independent of all the other possible system information.