Run the pipeline script directly

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 or get this on the command line by running pipelines/peppro.py --help). You just need to pass a few command-line parameters to specify: paired-end status, any prealignment genome indicies, primary genome name, index, and chromosome sizes assets, a sample name, an input file, and the output destination folder:

From the peppro/ repository folder (using the manually downloaded genome assets):

pipelines/peppro.py --single-or-paired single \
  --prealignment-index human_rDNA=default/b769bcf2deaf9d061d94f2007a0e956249905c64653cb5c8 \
  --genome hg38 \
  --genome-index default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 \
  --chrom-sizes default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.chrom.sizes \
  --sample-name test \
  --input examples/data/test_r1.fq.gz \
  -O peppro_test/

This example should take about 30 minutes to complete.

You can also run the pipeline directly at the command line using conda, a single container, or with the multi-container environment manager bulker.