when add autodie to gnos_upload_data.pl error is thown

[adamjohnwright]

I added this for diagnostic purposes but it seam to start throwing and error on opening and closing a DIR handle. This is something that should be looked at into the future

[keiranmraine]

Hi Adam,

You may find that it's complaining as you are using an unscoped variable for the handle:

https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow/blob/develop/workflow/scripts/gnos_upload_data.pl#L848

opendir(DIR, ".");

this should be at least:

opendir(my $dir, ".") || die;

autodie is based on much more recent standards so this could be the issue (but I can't say for certain).

A reason for avoiding bareword filehandles is better error messaging: http://modernperlbooks.com/mt/2011/07/why-the-modern-perl-book-avoids-bareword-filehandles.html

[adamjohnwright]

Hi Keiran,

Thanks for the suggestion. Yes, I would like to go through the code and make changes such as the one you are suggesting. I will discuss this with Brian and decide if we should be adding autodie back in with your suggested change. I am in favor of adding autodie and fixing the code that it is dying on.

Cheers, Adam