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Update fastqc runner #106

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Update fastqc runner #106

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c427202
Update fastqc
mgenereu Oct 4, 2022
8ed7129
Return the exit code
mgenereu Oct 4, 2022
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11 changes: 3 additions & 8 deletions fastqc
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ if ($threads) {
unshift @java_args,"-Xmx${used_memory}m";
}
else {
unshift @java_args,'-Xmx${memory}m';
unshift @java_args,"-Xmx${memory}m";
}

if ($kmer_size) {
Expand Down Expand Up @@ -346,13 +346,8 @@ if (@files or $version or $help) {

#warn "Running 'exec $java_bin,@java_args, \"uk.ac.babraham.FastQC.FastQCApplication\", @files, CLASSPATH is $ENV{CLASSPATH}";


if ($java_bin ne 'java') {
system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
}
else {
exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
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@mgenereu mgenereu Oct 4, 2022 •
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exec is designed to be very blind to the success or failure of the underlying process. "Fire and forget." Please review this change as I haven't seen system and exec mixed like this before and didn't understand the underlying reason.

}
system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
exit $? >> 8;

__DATA__

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