Comments (2)
One of the issues seems to be that calling gunzip from within the python script results in an empty vcf being created. However, 'gunzipping' the vcf.gz before running the python script works OK
from bovtb-nf.
Superseded by #5
from bovtb-nf.
Related Issues (18)
- Update trimmomatic version
- Python script read stdin
- Add run name to allow differentiation of the same sample sequenced multiple times
- Infer phlogenetic cluster in addition to genotype HOT 1
- Update Readme
- Update spoligotyping module to use standard names for spoligotypes HOT 2
- Update pipeline to use most recent version of M. bovis reference genome (LT708304) HOT 1
- VCF2Consensus process fails for some samples HOT 7
- Error in SNPfiltAnnot process HOT 1
- Add explanations to output for failure to assign WGS Cluster HOT 2
- Add process to ID samples that are not M. bovis HOT 1
- Bcftools consensus outputs reference base when data is missing
- Reliably detect M.bovis when it's at low prevalence in the sample HOT 3
- Output table of snps for each sample HOT 3
- Formatting of BovPos.tsv output needs correcting
- Using --lowmem option causes kraken2 to fail HOT 2
- Reduce failures for contaminated samples
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 bovtb-nf.