Looper: can't specify the individual path for one pipeline run
Looper does not generate any of these per-sample outputs.

Looper does not have any control over where your pipeline puts its outputs.

The problem is in your pipeline, not in looper. Assuming you're using a pypiper pipeline, I suggest reading the docs; for example, the "your first pipeline" tutorial: http://pypiper.readthedocs.io/en/latest/tutorials-first.html

For real-life example, see this pipeline


outfolder = os.path.abspath(os.path.join(args.output_parent, args.sample_name))
pm = pypiper.PipelineManager(name="RRBS", outfolder=outfolder, args=args, version=__version__)