Comments (4)
peterk87
commented on August 17, 2024
2
VADR annotation has been added in #73 and version 3.4.0. Hopefully that helps with your downstream needs @fanninpm!
from nf-flu.
peterk87
commented on August 17, 2024
1
@Codes1985 that's great to know! I wonder if staphb have a Conda channel since I don't seem to be getting anywhere with trying to update VADR in Bioconda. Bioconda MacOSX builds are the bane of my existence... I usually skip them for my own tools. I wonder if I can get away with adding an OSX skip in my PR.
from nf-flu.
peterk87
commented on August 17, 2024
Thanks @fanninpm for letting me know about VADR now supporting Influenza genome annotation.
It looks like the Bioconda package hasn't been updated in a while and v1.5.1 is the latest. I'll see if I can get it updated based on the changes in bioconda/bioconda-recipes#44370
from nf-flu.
Codes1985
commented on August 17, 2024
Just to follow up on this, I pulled the VADR singularity image from staphb, and I'm running it as a post-processing step after nf-flu finishes. So far it has been working well, and we are using it as part of our QC regime prior to uploading our data to GISAID.
from nf-flu.
Related Issues (20)
- Error running newly installed pipeline HOT 1
- [BUG]: Conda and Mamba profiles broken in 3.3.0 HOT 1
- [BUG]: no H/N subtypes assigned in subtyping reports with user-specified sequences HOT 1
- [BUG]: The fasta sequence does not match the REF allele at OQ234674.1:1946 HOT 3
- Emit concatenated, re-named .fastq files into subdirectory within the nf-flu results directory HOT 1
- [BUG]: Error executing process > 'NF_FLU:ILLUMINA:SUBTYPING_REPORT (1)' HOT 3
- [BUG]: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory HOT 3
- [BUG]: Mixed IAV and IBV run analysis reports all samples as IBV only HOT 4
- Optional dehosting
- Update README and docs for running nf-flu test profiles for Nanopore and Illumina platforms HOT 1
- [BUG]: ComputeError on SUBTYPING_REPORT HOT 4
- Read samplesheet.csv with fields as strong rather than inferred types
- Compatibility with cloud storage paths HOT 2
- Clair3 not variant calling ends of each segment HOT 4
- [BUG]: pull is only supported for shub URIs HOT 1
- Ability to output consensus sequences based on quality metrics (i.e., breadth and depth of coverage)
- [BUG]: nf-flu improperly labels segment ID for PB1 and PB2 for Influenza B HOT 3
- Better top reference selection from IRMA consensus seqs with high numbers of ambiguous bases
- [BUG]: CAT_ILLUMINA_FASTQ can mistakenly append 1:N:0:./2:N:0:. to quality score lines
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 nf-flu.