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), which you can also get on the command line by running pipelines/pepatac.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 a small test example through the pipeline:
From the pepatac/
repository folder (using the manually downloaded genome assets):
pipelines/pepatac.py --single-or-paired paired \
--prealignment-index rCRSd=default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4 \
--genome hg38 \
--genome-index default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 \
--chrom-sizes default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.chrom.sizes \
--sample-name test1 \
--input examples/data/test1_r1.fastq.gz \
--input2 examples/data/test1_r2.fastq.gz \
--genome-size hs \
-O $HOME/pepatac_test
This example should take about 20-30 minutes to complete.