NGS_run_summary

Download the directory:

git clone git@github.com:AWGL/ngs_run_summary.git

Create and activate the conda environment

conda env create -f ngs_run_summary.yml
conda activate ngs_run_summary

Requirements

Requires either:

• Access to NGS output directory which contains the run folders
• Access to a directory with copied run folders on local machine

Each run folder should contain:

• "InterOp" folder
• "RunParameters.xml" file
• "SampleSheet.csv" file

To run the programme

The code will need the "path" variable updating to the relevant directory containing the run folders.

To view help:

python ngs_run_summary.py -h

The programme will default to last months start and end date:

python ngs_run_summary.py

or an optional start and end date can be specified in the format YYMMDD:

python ngs_run_summary.py -s 210101 -e 210131

Additional info

• Code is set up to check for some logic problems with input dates and will report a STDOUT
• Output is a .csv file in the current directory
• Code will also STDOUT the start and end dates, along with a count of runs found within the range
• If no runs are found within date range then a blank .csv is output and a run count of 0 is displayed in STDOUT