Ecosyste.ms: Issues

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GitHub / molgenis/vip issues and pull requests

#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

#39 - Use module specific config files for module versions/default settings

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

#39 - Use module specific config files for module versions/default settings

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

#38 - Skip precomputed CADD scores for CAPICE

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

#38 - Skip precomputed CADD scores for CAPICE

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

#37 - Fix #36 Use CAPICE precomputed scores

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

#36 - Use CAPICE precomputed scores

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

#36 - Use CAPICE precomputed scores

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

#35 - Decide how to deal with existing annotations

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

#34 - Test sh is version dependent

Issue - State: closed - Opened by bartcharbon over 4 years ago - 1 comment
Labels: bug

#34 - Test sh is version dependent

Issue - State: closed - Opened by bartcharbon over 4 years ago - 1 comment
Labels: bug

#33 - Fix #32 Module unload doesn't unload dependencies

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

#33 - Fix #32 Module unload doesn't unload dependencies

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

#32 - Module unload doesn't unload dependencies

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

#32 - Module unload doesn't unload dependencies

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

#31 - Clean up test data

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

#31 - Clean up test data

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

#30 - Add extra logging to test (started, extra failure info, finished)

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

#30 - Add extra logging to test (started, extra failure info, finished)

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

#29 - Add default VEP plugin dir

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

#29 - Add default VEP plugin dir

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

#28 - Post-processing step

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

#28 - Post-processing step

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

#27 - Split pipeline in modules that can be called seperately

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

#27 - Split pipeline in modules that can be called seperately

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

#26 - Fix #17 Command-line option --ann_vep to pass VEP args

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

#25 - Annotate variants with MVL

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

#24 - Fix #7: Add test scripts for semi-automated testing

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

#24 - Fix #7: Add test scripts for semi-automated testing

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

#23 - Fix #22 Annotate input vcf with VKGL classification

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

#23 - Fix #22 Annotate input vcf with VKGL classification

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

#22 - Annotate input vcf with VKGL classification

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

#21 - Fix #16 Decompose and normalize records before annotation

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

#20 - Fix HPO prefix in examples

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

#20 - Fix HPO prefix in examples

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

#19 - Replace hardcoded paths

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

#17 - Command-line option --ann_vep to pass additional VEP args

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

#17 - Command-line option --ann_vep to pass additional VEP args

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

#16 - Decompose and normalize records before annotation

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

#16 - Decompose and normalize records before annotation

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

#15 - Command-line option -fa --fasta for reference sequence

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

#15 - Command-line option -fa --fasta for reference sequence

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

#14 - Fix module versions to increase reproducability

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

#12 - Fix #11 Add SBATCH directives to pipeline.sh

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

#11 - Add default batch script submission options

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

#10 - Keep variants that fail validation and keep non-variants

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

#9 - Keep variants without a CAPICE score

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

#8 - CAPICE annotations could be missing for INDELs

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

#7 - Add test scripts for semi-automated testing

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

#6 - Allow modules to be called separately

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

#5 - Improve error handling

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

#4 - Replace with capice2vcf.jar with module artifact

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

#3 - All logging to stdout en stderr

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

#2 - Use vcf-report module instead of vip-report

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

#1 - Add capice and VcfAnno

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