=head1 Let's Find Some Samples
Possibly the most important part of your workflow is finding samples.
Samples, like variables, come in two flavors. They are files, or they are
directories. The first shows files, and the second directories.
=head1 Examples!
=head2 Samples are Files
=head3 Directory Structure
Samples are files
with
the sample name and a .csv extension.
bash
/home/user/workflow/
/data
/raw
sample1.csv
sample2.csv
=head3 Workflow Configuration
yaml
---
global:
- indir: /home/user/workflow/data/raw
- outdir: /home/user/workflow/data/analysis
- file_rule: (sample.*).csv$
=head2 Samples are Directories
This
time
the sample names come from a directory,
with
stuff inside.
=head3 Directory Structure
yaml
/path/to/indir
/sample1
billions_of_small_files
from_the_Sequencer
/sample2
billions_of_small_files
from_the_Sequencer
=head3 Workflow Configuration
yaml
---
global:
- indir: /home/user/workflow/data/raw
- outdir: /home/user/workflow/data/analysis
- file_rule: (sample.*)
- find_by_dir: 1
- by_sample_outdir: 1