Running the pipeline script directly

It's easiest to run PEPPRO using looper, as described in the install and tutorial guides. This simplifies running the pipeline across many samples, on a cluster, or in containers. But really, the pipeline at its core is just a python script, and you can run it on the command line for a single sample (see command-line usage by running pipelines/ --help). You just need to pass a few command-line parameters to specify sample name, reference genome, input files, etc. Here's the basic command to run the included small test example through the pipeline:

cd peppro
./pipelines/ \
  --sample-name test \
  --genome hg38 \
  --input examples/data/test_r1.fq.gz \
  --single-or-paired single \
  -O $HOME/peppro_example/

This test example takes less than 5 minutes to complete.