Workstation Housekeeping

Utilities for managing data on the local NGS workstation

Reference

• wscleaner
• backup_runfolder.py
• findfastqs.sh

---

wscleaner

Clear NGS runfolders that are backed up in DNANexus.

wscleaner --set-key DNA_NEXUS_KEY # Cache dnanexus api key
wscleaner ROOT_DIRECTORY --logfile LOGFILE_PATH

---

backup_runfolder.py

Upload a directory to a DNANexus project.

backup_runfolder.py [-h] -i RUNFOLDER [-a AUTH_TOKEN] [--ignore IGNORE] [-p PROJECT] [--logpath LOGPATH]

---

findfastqs.sh

Report the number of gzipped fastq files in an directory.

$ findfastqs.sh RUNFOLDER
>>> RUNFOLDER has 156 demultiplexed fastq files with 2 undetermined. Total: 158