The code in its current form fails whenever readgroup is set to 0 by design:
@RG ID=0
Read groups from Illumina/Isaac pipeline are typically numbered 0, 1, 2, ...
If you want to use unless, you need to make an exception for RG==0, e.g.
my $bas_ob_rg=$bas_ob->get($rg_id, 'readgroup');
unless($bas_ob_rg==0 || $bas_ob_rg) { die "Readgroup $rg_id in bam file but not in bas file $!"; }
Traceback from inside dockstore-cgpwgs-2.0.1.simg
Readgroup 0 in bam file but not in bas file at /opt/wtsi-cgp/bin/brassI_prep_bam.pl line 146. Command exited with non-zero status 255
The code in its current form fails whenever readgroup is set to 0 by design:
@RG ID=0
Read groups from Illumina/Isaac pipeline are typically numbered 0, 1, 2, ...https://github.com/cancerit/BRASS/blob/d08d1746a2db65f86a2febf4f947185c0d61b003/perl/bin/brassI_prep_bam.pl#L146
If you want to use unless, you need to make an exception for RG==0, e.g.
Traceback from inside dockstore-cgpwgs-2.0.1.simg
Readgroup 0 in bam file but not in bas file at /opt/wtsi-cgp/bin/brassI_prep_bam.pl line 146. Command exited with non-zero status 255