molgenis data-transform-vkgl issues

molgenis / data-transform-vkgl

GNU Lesser General Public License v3.0

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Use `GCA_000001405.15_GRCh38_no_alt_analysis_set` as `GRCh38` reference

#69 dennishendriksen opened 7 months ago
0
feat: improve run.sh to make it work better

#68 dtroelofsprins opened 1 year ago
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fix: update to make it work

#67 dtroelofsprins opened 1 year ago
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chore(deps): bump guava from 30.0-jre to 32.0.0-jre

#66 dependabot[bot] opened 1 year ago
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Variants deleted in clinvar and later updated again, should be "update" rather than "novel"

#65 marikaris closed 2 years ago
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Pseudogenes should not be submitted as such to ClinVar

#64 marikaris closed 2 years ago
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Last lab to be transformed by `run.sh` output gets cut off

#63 marikaris opened 2 years ago
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Use ftp server for data delivery

#62 bartcharbon closed 2 years ago
2
Fix #60 Valid withdrawn genes using alias or previous symbols

#61 dennishendriksen closed 2 years ago
2
Valid withdrawn genes using alias or previous symbols

#60 dennishendriksen closed 2 years ago
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docs: add release info

#59 marikaris closed 3 years ago
2
Add liftover script for consensus files

#58 bartcharbon closed 3 years ago
2
Test checklist

#57 bartcharbon closed 3 years ago
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Create pull_request_template.md

#56 marikaris closed 3 years ago
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Integration tests broken

#55 marikaris closed 2 years ago
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fix: set null string for csv

#54 marikaris opened 3 years ago
2
introduce vkgl_consensus_add_gene_id.sh

#53 dennishendriksen closed 3 years ago
2
Treat gene symbols with incorrect casing as invalid

#52 dennishendriksen opened 3 years ago
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chore: remove termcolor

#51 marikaris closed 3 years ago
2
feat: add script that prepares the output of run.sh for molgenis-py-consensus

#50 marikaris opened 3 years ago
2
Genes with invalid HGNC symbols are always written to errorfile

#49 marikaris opened 3 years ago
0
Variant identifiers change when gene symbols change

#48 dennishendriksen opened 3 years ago
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fix: fix grep for done log with >9 logs

#47 marikaris closed 3 years ago
2
fix(data-release-pipeline): change the done check in run.sh

#46 marikaris closed 3 years ago
2
feat(release script): add vkgl release script and validation script

#45 marikaris closed 3 years ago
2
Fix #35: Potential fix

#44 bartcharbon closed 3 years ago
2
Fix: Missing variants when processing multiple labs at once

#43 dennishendriksen closed 3 years ago
2
Pipeline outputs "" for empty timestamp input

#42 dennishendriksen opened 3 years ago
0
Revert "Consensus generator command-line app"

#41 dennishendriksen closed 3 years ago
0
Consensus generator command-line app

#40 dennishendriksen closed 3 years ago
3
Variant validator has issues with delins that's possibly an inversion

#39 marikaris opened 3 years ago
0
When several cdna/transcripts are specified, the cdna in the LUMC route gets messed up

#38 marikaris opened 3 years ago
2
chore(deps): bump commons-io from 2.6 to 2.7

#37 dependabot[bot] closed 3 years ago
2
Variants that are reported twice, once with the correct gene and once with an outdated one, are not reported as duplicate

#36 marikaris closed 3 years ago
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When internet connection is lost and batch of variants is not returned from variant validator, no error is presented

#35 marikaris closed 3 years ago
2
fix(pom.xml): set java and maven compiler plugin version

#34 marikaris closed 3 years ago
1
fix(pom.xml): set version of maven-compiler-plugin

#33 marikaris closed 3 years ago
1
feat: add gene validation service

#32 marikaris closed 3 years ago
1
Fix: variants mapped incorrectly when anchor is right from variant and anchor is equal to nucleotide change

#31 marikaris closed 3 years ago
2
Fix/14 incorrect variants

#30 marikaris closed 3 years ago
2
Bump Guava 20.0 to 30.0-jre (fix CVE-2018-10237 alert)

#29 dennishendriksen closed 3 years ago
2
Variant formatter reports 'Failed to fetch from SeqRepo' errors

#28 dennishendriksen opened 3 years ago
0
Build stability warnings

#27 dennishendriksen closed 3 years ago
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Variant formatter uses transcript db older than db used by labs

#26 dennishendriksen opened 4 years ago
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Variant formatter uses GRCh37 instead of GRCh37.p13

#25 dennishendriksen opened 4 years ago
1
Fix/20 21 code dup doc

#24 marikaris closed 4 years ago
2
Fix/14 incorrect variants

#23 marikaris closed 3 years ago
3
Variants are rejected with "skipping variant due to error 'x': not a variant: x"

#22 bartcharbon opened 4 years ago
0
Missing documentation for hgvs translator flags

#21 dennishendriksen closed 4 years ago
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hgvs translator code duplication

#20 dennishendriksen closed 4 years ago
0