BioX::Workflow::Command::run::Utils::Samples

Variables

Subroutines

get_samples

Get basename of the files. Can add optional rules.

sample.vcf.gz and sample.vcf would be sample if the sample_rule is (.vcf)$|(.vcf.gz)$

Also gets the full path to infiles

Instead of doing

    foreach my $sample (@$self->samples){
        dostuff
    }

Could have

    foreach my $infile (@$self->infiles){
        dostuff
    }

match_samples

Match samples based on regex written in sample_rule

process_by_sample_outdir

Make sure indir/outdirs are named appropriated for samples when using by