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monarch-initiative
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pheval.exomiser
Exomiser plugin for PhEval.
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pheval-exomiser prepare-exomiser-batch command bugs
#61
AO33
opened
1 month ago
1
59 allow for multiple output formats from exomiser
#60
yaseminbridges
closed
1 month ago
1
Allow for multiple output formats from Exomiser
#59
yaseminbridges
closed
1 month ago
3
57 exomiser v14 whitelist option in application.properties
#58
yaseminbridges
closed
4 months ago
1
Exomiser v14 whitelist option in application.properties
#57
yaseminbridges
closed
4 months ago
0
Setting the Exomiser raw output filename
#56
yaseminbridges
closed
4 months ago
0
Write out exomiser result prefix as the name of the phenopacket
#55
yaseminbridges
closed
4 months ago
0
53 trim exomiser from pheval result tsv file names
#54
yaseminbridges
closed
7 months ago
0
trim `-exomiser` from pheval result tsv file names
#53
yaseminbridges
closed
7 months ago
0
51 add acmg check for variant results
#52
yaseminbridges
closed
4 months ago
0
add acmg check for variant results
#51
yaseminbridges
closed
4 months ago
0
49 remove usrbinjava from command used to invoke exomiser
#50
yaseminbridges
closed
10 months ago
0
Remove `/usr/bin/java` from command used to invoke Exomiser
#49
yaseminbridges
closed
10 months ago
0
47 add support for separated gene analysis and variant analysis fields in config
#48
yaseminbridges
closed
11 months ago
0
Add support for separated `gene_analysis` and `variant_analysis` fields in config
#47
yaseminbridges
closed
11 months ago
0
removing exomiser_software_directory variable
#46
yaseminbridges
opened
1 year ago
0
Remove `exomiser_software_directory` property from runner config.yaml
#45
yaseminbridges
opened
1 year ago
0
42 include disease prioritisation results for exomiser runner
#44
yaseminbridges
closed
1 year ago
0
41 update documentation for runner
#43
yaseminbridges
closed
1 year ago
0
Include disease prioritisation results for Exomiser runner
#42
yaseminbridges
closed
1 year ago
0
Update documentation for runner
#41
yaseminbridges
closed
1 year ago
0
Avoid index usage for phenopacket and vcf directory for batch file preparation
#40
yaseminbridges
closed
1 year ago
0
Avoid index usage in phenopackets_dir during batch file preparation
#39
souzadevinicius
closed
1 year ago
0
23 move the contents within the runner config to the input dir config
#38
yaseminbridges
closed
1 year ago
0
changing VCF to vcf in fileFormat phenopacket testdata
#37
yaseminbridges
closed
1 year ago
0
fix test data in test_create_batch_commands.py
#36
yaseminbridges
closed
1 year ago
0
trim `-exomiser` from post-processed result file name before writing
#35
yaseminbridges
closed
1 year ago
0
Strip `-exomiser` from file written in post-processed results
#34
yaseminbridges
closed
1 year ago
0
Strip angled brackets from Exomiser json `alt` field
#33
yaseminbridges
closed
1 year ago
1
strip angled brackets from exomiser json results
#32
yaseminbridges
closed
1 year ago
0
30 fix variable inputs to create standardised results method
#31
yaseminbridges
closed
1 year ago
1
Fix variable inputs to create_standardised_results method
#30
yaseminbridges
closed
1 year ago
0
28 implement new post processing methods
#29
yaseminbridges
closed
1 year ago
0
implement new post-processing methods
#28
yaseminbridges
closed
1 year ago
0
implement methods to run on the GEL RE
#27
yaseminbridges
closed
1 year ago
1
implement methods to run on Apocrita
#26
yaseminbridges
closed
1 year ago
1
run in different environments
#25
yaseminbridges
closed
1 year ago
0
11 write exomiser applicationproperties
#24
yaseminbridges
closed
1 year ago
0
Move the contents within the runner config to the input dir config
#23
yaseminbridges
closed
1 year ago
0
update runner to use version variable supplied in the run command
#22
yaseminbridges
closed
1 year ago
0
15 collapse all write local and write docker methods
#21
yaseminbridges
closed
1 year ago
0
14 fix path in test run.py
#20
yaseminbridges
closed
1 year ago
0
16 add docker mounted volume paths to constants.py
#19
yaseminbridges
closed
1 year ago
5
12 remove exomiser filename suffix from constants
#18
yaseminbridges
closed
1 year ago
0
removing test file containing hashed out tests for the CLI runner
#17
yaseminbridges
closed
1 year ago
0
Add docker mounted volume paths to constants.py
#16
yaseminbridges
closed
1 year ago
2
Collapse all write local and write docker methods
#15
yaseminbridges
closed
1 year ago
0
fix path in test_run.py
#14
yaseminbridges
closed
1 year ago
0
remove hashed code from CLI tests
#13
yaseminbridges
closed
1 year ago
0
Remove exomiser filename suffix from constants
#12
yaseminbridges
closed
1 year ago
0
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