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.

Examples!

Samples are Files

Directory Structure

Samples are files with the sample name and a .csv extension.

 bash
     /home/user/workflow/
         /data
             /raw
                 sample1.csv
                 sample2.csv

Workflow Configuration

 yaml
     ---
     global:
         - indir: /home/user/workflow/data/raw
         - outdir: /home/user/workflow/data/analysis
         - file_rule: (sample.*).csv$

Samples are Directories

This time the sample names come from a directory, with stuff inside.

Directory Structure

 yaml
     /path/to/indir
         /sample1
             billions_of_small_files
             from_the_Sequencer
         /sample2
             billions_of_small_files
             from_the_Sequencer

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