Comments (7)
Below is a graph of the average time a process takes. This one is from mid-September. The process that takes the longest to run per sample is Freyja.
There was an attempt to alleviate this problem in version 3.820230926 by requiring a minimum depth. This hasn't really made an impact, however.
from cecret.
I have thought about dropping Freyja boot.
from cecret.
from cecret.
If you don't need the results from Freyja, you can change the freyja parameter to false.
In a config file add a params.freyja = false
line, and on the command line it's something like
nextflow run UPHL-BioNGS/Cecret <everything else you normally run> --freyja false
This should skip Freyja altogether?
from cecret.
from cecret.
I'm not sure. I didn't even notice until this summer, so I'm thinking it's something with version 1.4.5+.
from cecret.
As an update to this issue, I have created a PR where freyja boot
has been removed : #250
This makes the workflow much faster.
As soon as this PR passes testing, we'll merge it and it will be the default workflow.
from cecret.
Related Issues (20)
- Version check
- Nextclade will break workflow on January 16
- Version check
- Version check HOT 1
- Producing snps and trees from Covid reads input HOT 20
- Version check HOT 1
- Version check
- Version check HOT 1
- Add pango-collapse.txt HOT 1
- Version check HOT 1
- Add GA test for bbnorm
- Fix kraken2 classified and unclassified reads HOT 1
- Version check HOT 1
- Version check HOT 1
- Version check
- Version check
- Version check
- Setting a minimum variant cutoff for Freyja HOT 2
- Version check
- Version check
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cecret.