This directory contains files, scripts, etc. related to processing NextSeq-generated sequencing data.
The main script to launch the pipeline is process_sequencing_run.py
To view the current list of input args and explanations, type '-h' as the first argument to the script.
A printout will give the required and optional input args.
As of March 3, 2015:
usage: process_sequencing_run.py [-h] -r RUN_DIRECTORY [-e RECIPIENTS]
optional arguments:
-h, --help show this help message and exit
-r RUN_DIRECTORY, --rundir RUN_DIRECTORY
The full path to the run directory
-e RECIPIENTS, --email RECIPIENTS
Comma-separated list of email addresses for
notifications (no spaces between entries)
The '-r' arg is followed by the full path to the sequencing output directory created by the instrument:
e.g.
/ifs/labs/cccb/projects/cccb/instruments/NS500749/150211_NS500749_0002_AH5GMMBGXX
The '-e' arg is followed by a comma-separated list of email addresses that will be notified when the run is complete
(including the external data delivery links). No spaces between the entries, as shown below:
e.g.
abc@jimmy.harvard.edu,def@jimmy.harvard.edu
Additional notes:
The script (and subprocesses that are launched) will send logging to stdout, so this should be captured in a nohup.out log or similar redirection.
Update March 6, 2017:
All the above is still relevant.
blawney/demux_pipeline
Demultiplex and project structure for automatic processing of sequence data.
Python