genomic-medicine-sweden / jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

https://jasen.readthedocs.io/en/latest/

GNU General Public License v3.0

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299 add qc for nanopore data #344

Open Emkago opened 2 months ago

Emkago commented 2 months ago

Description

Added module with NanoPlot to check quality of raw input reads produced by ONT technology.

Summary of the changes made: added new module script, added container URL to Makefile, changed bacterial base workflow script

Primary function of PR

[ ] Hotfix
[x] Minor functionality improvement
[ ] Major functionality improvement / New type of analysis
[ ] Backward-breaking functionality

Testing

The pipeline has been run with test data, NanoPlot report is produced in the nanoplot output folder.

Sign-offs

[ ] Code reviewed by @octocat
[ ] Code tested by @octocat

Emkago commented 2 months ago

Confusion with commits, need to check what happened before reviewing and merging

ryanjameskennedy commented 2 months ago

No worries, make it a draft until you're ready for review, so we don't use the CI resources:)