Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / molgenis/vip issues and pull requests

#101 - Bump report(1.5.0) and pipeline (1.6.0) version

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#100 - Add arguments to pass onto preprocessing or report

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#100 - Add arguments to pass onto preprocessing or report

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#99 - Add flag to switch hpo inheritance annotation on.

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#99 - Add flag to switch hpo inheritance annotation on.

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#97 - HPO plugin incorrect if genes_to_phenotype.txt has exactly three cols

Issue - State: closed - Opened by dennishendriksen about 4 years ago
Labels: bug

#97 - HPO plugin incorrect if genes_to_phenotype.txt has exactly three cols

Issue - State: closed - Opened by dennishendriksen about 4 years ago
Labels: bug

#96 - Fix #77 Write pipeline version and command to output

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#96 - Fix #77 Write pipeline version and command to output

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#95 - update inheritance plugin to HPO based matching

Pull Request - State: closed - Opened by bartcharbon about 4 years ago - 1 comment

#95 - update inheritance plugin to HPO based matching

Pull Request - State: closed - Opened by bartcharbon about 4 years ago - 1 comment

#93 - update inheritance matcher version

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#92 - Add SpliceAI plugin

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#91 - update report and matcher dependency versions + expected html

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#90 - Release/1.4.0

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#90 - Release/1.4.0

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#88 - Add inheritance module

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#87 - Move Inheritance plugin to this repo

Pull Request - State: closed - Opened by bartcharbon about 4 years ago

#86 - VEP plugin to annotate transcripts with a HPO flag

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#86 - VEP plugin to annotate transcripts with a HPO flag

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#85 - Preferred transcript plugin: ignore transcript versions

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#84 - Use non-public VKGL annotation file with 5-class system

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#83 - Fix #81 --ann_vep broken

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#82 - VEP plugin to annotate transcripts with a PREFERRED flag

Pull Request - State: closed - Opened by dennishendriksen about 4 years ago

#81 - --ann_vep broken since v1.2.0

Issue - State: closed - Opened by dennishendriksen about 4 years ago
Labels: bug

#80 - Error pre-processing VCF in case of missing DP format header

Issue - State: closed - Opened by dennishendriksen about 4 years ago
Labels: bug

#80 - Error pre-processing VCF in case of missing DP format header

Issue - State: closed - Opened by dennishendriksen about 4 years ago
Labels: bug

#79 - Remove low quality reads removed by default

Issue - State: closed - Opened by dennishendriksen about 4 years ago - 1 comment

#79 - Remove low quality reads removed by default

Issue - State: closed - Opened by dennishendriksen about 4 years ago - 1 comment

#77 - Write pipeline version and arguments in VCF header

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: enhancement

#77 - Write pipeline version and arguments in VCF header

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: enhancement

#76 - Fix #51 Pipeline fails for paths with spaces

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#76 - Fix #51 Pipeline fails for paths with spaces

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#75 - Fix #64 Annotate symbol source by default

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#74 - Filter low-quality VCF records

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#73 - Fix #72 Probands input argument

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#73 - Fix #72 Probands input argument

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#72 - Probands input argument

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: enhancement

#71 - Remove --gene_phenotype from default annotation arguments

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: enhancement

#70 - Bash wrapper script to improve usage in Easybuild env

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 2 comments
Labels: enhancement

#70 - Bash wrapper script to improve usage in Easybuild env

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 2 comments
Labels: enhancement

#68 - Fix #65 Fallback to CADD/v1.4-foss-2018b-minimal (backport)

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#66 - Fix #65 Use CADD/v1.4-foss-2018b-minimal when available

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#66 - Fix #65 Use CADD/v1.4-foss-2018b-minimal when available

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#65 - Use CADD/v1.4-foss-2018b-minimal when available

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: enhancement

#65 - Use CADD/v1.4-foss-2018b-minimal when available

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 1 comment
Labels: enhancement

#64 - Annotate symbol source by default

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: enhancement

#64 - Annotate symbol source by default

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: enhancement

#63 - Fix #14 Fix module versions (backport)

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#63 - Fix #14 Fix module versions (backport)

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#61 - Added #60 Check if all modules are available before running pipeline.

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#60 - Check if all modules are available before running pipeline.

Issue - State: closed - Opened by svandenhoek over 4 years ago - 1 comment
Labels: enhancement

#60 - Check if all modules are available before running pipeline.

Issue - State: closed - Opened by svandenhoek over 4 years ago - 1 comment
Labels: enhancement

#59 - Fix #14 Fix module versions (backport)

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#59 - Fix #14 Fix module versions (backport)

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#58 - Update vcf-report v1.0.2 to v1.0.3

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#58 - Update vcf-report v1.0.2 to v1.0.3

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#57 - Fix #14 Fix module versions

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#57 - Fix #14 Fix module versions

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#56 - Improved decision tree

Pull Request - State: closed - Opened by bartcharbon over 4 years ago

#56 - Improved decision tree

Pull Request - State: closed - Opened by bartcharbon over 4 years ago

#55 - Pipeline option to use custom decision tree

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#55 - Pipeline option to use custom decision tree

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#54 - Add MVL annotations

Pull Request - State: closed - Opened by bartcharbon over 4 years ago

#54 - Add MVL annotations

Pull Request - State: closed - Opened by bartcharbon over 4 years ago

#53 - Remove existing annotations that are added by the pipeline

Pull Request - State: closed - Opened by bartcharbon over 4 years ago

#52 - Annotate non-coding variants & add allele numbers

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#52 - Annotate non-coding variants & add allele numbers

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#51 - Pipeline fails for paths with spaces

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: bug

#51 - Pipeline fails for paths with spaces

Issue - State: closed - Opened by dennishendriksen over 4 years ago
Labels: bug

#50 - Update to fix for #40 -> now as oneliner

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#49 - Variant classification using vcf-decision-tree

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#49 - Variant classification using vcf-decision-tree

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#48 - Update VKGL annotations

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 2 comments
Labels: enhancement

#48 - Update VKGL annotations

Issue - State: closed - Opened by dennishendriksen over 4 years ago - 2 comments
Labels: enhancement

#47 - Added a basic pull request template

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#47 - Added a basic pull request template

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#46 - Code improvements.

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#46 - Code improvements.

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#45 - Add functions to bash scripts

Issue - State: closed - Opened by svandenhoek over 4 years ago - 1 comment
Labels: enhancement

#45 - Add functions to bash scripts

Issue - State: closed - Opened by svandenhoek over 4 years ago - 1 comment
Labels: enhancement

#44 - Fixes #40 for introduced sbatch issues

Pull Request - State: closed - Opened by svandenhoek over 4 years ago - 1 comment

#44 - Fixes #40 for introduced sbatch issues

Pull Request - State: closed - Opened by svandenhoek over 4 years ago - 1 comment

#43 - Added .gitignore file.

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#43 - Added .gitignore file.

Pull Request - State: closed - Opened by svandenhoek over 4 years ago

#42 - Fix #38 Skip precomputed CADD scores for CAPICE

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#42 - Fix #38 Skip precomputed CADD scores for CAPICE

Pull Request - State: closed - Opened by dennishendriksen over 4 years ago

#40 - Script fails when trying to run from a different directory.

Issue - State: closed - Opened by svandenhoek over 4 years ago - 3 comments
Labels: bug