genome-nexus genome-nexus-annotation-pipeline issues

genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API

MIT License

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issues

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Add consequence for IGR variants

#282 leexgh opened 1 week ago
0
Readd docker gnap wrapper

#281 hweej opened 2 weeks ago
0
Add gnap wrapper for docker build

#280 hweej closed 2 weeks ago
0
Docker image improvements

#279 hweej closed 1 month ago
0
Error report misses '/' in URL column

#278 leexgh opened 3 months ago
0
Singularity 3.7 got LinkageError when running master

#277 leexgh opened 3 months ago
0
Singularity 3.3 cannot pull master docker

#276 leexgh opened 3 months ago
0
Documentation for application.properties overrides via ENV variables

#275 hweej opened 3 months ago
0
Handling Intergenic Variants in the MAF: Annotation Pipeline doesn't fill out any columns when VEP returns no transcript

#274 rmadupuri opened 4 months ago
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Add grch38 usage document

#273 leexgh closed 5 months ago
0
Upgrade to java 21

#272 mandawilson closed 3 months ago
4
Error when having duplicated variants and no end positions

#271 leexgh opened 5 months ago
0
Return non-zero exit code when annotation pipeline fails

#270 jamesqo closed 5 months ago
0
Fix typo in README.md

#269 kojix2 closed 2 months ago
0
Tumor_Seq_Allele1 and Tumor_Seq_Allele2 should be the same

#268 leexgh opened 8 months ago
0
Java11 updates

#267 callachennault closed 8 months ago
1
Add command parameter groups

#266 leexgh opened 9 months ago
0
Add '-n' note column in maf and error message into error report

#265 leexgh closed 9 months ago
3
Revert docker image back to executable form to maintain old usage.

#264 hweej closed 10 months ago
0
Turn on replace-symbol-entrez by default

#263 leexgh closed 9 months ago
1
entrypoint to cmd switch breaks old usage of cli

#262 inodb opened 10 months ago
0
Update README

#261 leexgh closed 10 months ago
0
Handling variants with common prefixes between GENIE and public GN

#260 rmadupuri opened 10 months ago
1
Some complex variants with common prefix - suffix fail the annotation

#259 rmadupuri opened 10 months ago
0
Error runnnig docker on v1.0.0

#258 aclosa closed 10 months ago
3
Adding sift and polyphen causes all annotations fail

#257 leexgh closed 10 months ago
0
Fix unsupported enrichment fields in query

#256 leexgh closed 10 months ago
0
Add note column to include some important comments

#255 leexgh closed 9 months ago
0
Add a new command parameter to set oncokb token

#254 leexgh opened 11 months ago
0
Add procps for ps command

#253 hweej closed 11 months ago
0
Add support for oncokb annotation

#252 sivkovic closed 11 months ago
0
Add server version to version sub command

#251 inodb closed 11 months ago
0
Change ENTRYPOINT to CMD for run flexibility

#250 hweej closed 11 months ago
0
Bump h2 from 1.3.156 to 2.2.220

#249 dependabot[bot] opened 12 months ago
0
CTNNB1 annotation fails but direct genome nexus API call succeed

#248 leexgh opened 1 year ago
0
Add new flag for logging verbosity and log output location

#247 leexgh opened 1 year ago
2
Bump sqlite-jdbc from 3.34.0 to 3.41.2.2

#246 dependabot[bot] opened 1 year ago
0
Fix log4j configuration in docker

#245 leexgh closed 1 year ago
1
Turn on logging for genome-nexus runs

#244 japerez-cls closed 1 year ago
0
test failures building the project annotationPipeline

#243 ldelgado-serrano opened 1 year ago
1
Add client version as subcommand

#242 inodb closed 11 months ago
1
Add mvn-external-version

#241 inodb closed 1 year ago
0
Update cbioportal dependency

#240 callachennault closed 1 year ago
0
Fix logback conflict

#239 leexgh closed 1 year ago
0
Latest build of genomenexus/gn-annotation-pipeline:master is non-functional, even when using the toy example on https://docs.genomenexus.org/annotate-file

#238 pwaltman closed 1 year ago
1
Improve dockerhub documentation

#237 pieterlukasse opened 1 year ago
0
Update to use new InfoController/Version Schema

#236 averyniceday closed 1 year ago
0
cBioPortal v5.2.0

#235 dippindots closed 1 year ago
0
whitespace

#234 Luke-Sikina opened 1 year ago
0
Support not removing matching bases and sticking with original input

#233 leexgh closed 1 year ago
2