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/peppro.py --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/peppro.py \ --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.