TYMichaelsen covid19 issues

TYMichaelsen / covid19

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK

GNU General Public License v3.0

3 stars 3 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Publish the Covid-19 Data in Denmark as KG

#48 tomersagi opened 3 years ago
1
Microreact integration

#47 MiroPakanec opened 3 years ago
0
Create a mockup of the website with Mads and Thomas

#46 tomersagi opened 4 years ago
1
Create a script to run the full pipeline to microreact

#45 tomersagi opened 4 years ago
0
Count cases per region in the original Danish metadata and filter microreact output accordingly

#44 tomersagi opened 4 years ago
4
Create an nwk file for microreact

#43 tomersagi closed 4 years ago
0
Create next-strain csv file

#42 tomersagi closed 4 years ago
3
map is not included in .svg auspice

#41 TYMichaelsen opened 4 years ago
0
Figure out how to get adhoc markers from Excel such as the mink case in /srv/rbd/covid19/metadata/raw-ssi-metadata/2020-06-29_nordjylland-case.xlsx

#40 tomersagi opened 4 years ago
0
Clade ingestion fails to create edges with people

#39 tomersagi opened 4 years ago
0
Create ingestion process for international clade file

#38 tomersagi closed 4 years ago
1
What happens to the fastq in /processing/ after livebasecalling is done?

#37 TYMichaelsen opened 4 years ago
0
Enable tranmission lines for local aupsice

#36 biocyberman opened 4 years ago
0
added dates as bool fields

#35 tomersagi closed 4 years ago
0
Cleansing script is not outputting parish code for any case

#34 tomersagi closed 4 years ago
0
Review Table 1 from the paper and report the same thing.

#33 tomersagi closed 4 years ago
0
Add a relation between clades

#32 tomersagi closed 4 years ago
0
Move wiki ssi schema to a secure google doc

#31 tomersagi closed 4 years ago
1
add message for barcode-match

#30 TYMichaelsen opened 4 years ago
0
Iss19

#29 tomersagi closed 4 years ago
0
Add PPHMyAdmin to the MySQL server container

#28 tomersagi closed 4 years ago
1
Reclassify GISAID data to match the Danish strain naming system

#27 tomersagi opened 4 years ago
0
Add bloom over neo4j

#26 tomersagi opened 4 years ago
8
Create wiki page for neo4j users

#25 tomersagi opened 4 years ago
0
Add low/high SES regions to neo4j data

#24 tomersagi closed 4 years ago
2
Add global nextstrain data to neo4j

#23 tomersagi opened 4 years ago
0
Metadata contains supicous pregnancy data

#22 tomersagi closed 4 years ago
3
Add script that changes ulimit and then runs neo4j

#21 tomersagi opened 4 years ago
0
Create data cleansing script

#20 tomersagi closed 4 years ago
4
Create conversion script for metadata to neo4j and mysql format

#19 tomersagi closed 4 years ago
3
Create mySQL instance singularity container

#18 tomersagi closed 4 years ago
3
Cannot connect to Neo4J instance created from sif file

#17 tomersagi closed 4 years ago
3
Create singularity container for Pentaho BI

#16 tomersagi opened 4 years ago
8
Creating cingularity sif file for pentaho fails

#15 tomersagi closed 4 years ago
1
Develop

#14 SorenKarst closed 4 years ago
0
covid19_workflow.sh needs full path to input folder to work - should be relative path

#13 TYMichaelsen closed 4 years ago
1
Quite some changes on nextstrain.sh, nextwrap.sh

#12 biocyberman closed 4 years ago
0
Merge with master

#11 SorenKarst closed 4 years ago
0
Add extractGenome.sh for extracting a subset of genome sequences

#10 biocyberman closed 4 years ago
0
Update auspiceView.sh, add auspice-init service, covid19_path.sh

#9 biocyberman closed 4 years ago
0
Add seqtk

#8 biocyberman closed 4 years ago
0
Some improvements

#7 biocyberman closed 4 years ago
0
Update to work with new metadata, and add Pangolin

#6 biocyberman closed 4 years ago
0
Recover nextrains.sh

#5 biocyberman closed 4 years ago
0
Add pandoc, and example for installing additional packages

#4 biocyberman closed 4 years ago
4
Add README for build and tweak Makefile for faster subsequent builds

#3 biocyberman closed 4 years ago
1
Some improvement

#2 biocyberman closed 4 years ago
1
add install CUDA host driver

#1 biocyberman closed 4 years ago
0