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fix: ensure the #CHROM is not quoted #896

Merged
merged 4 commits into from
Nov 5, 2024
Merged

fix: ensure the #CHROM is not quoted #896

merged 4 commits into from
Nov 5, 2024

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project-defiant
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@project-defiant project-defiant commented Nov 4, 2024

✨ Context

The output from convertToVcf step uses the csv writer which can not write the #CHROM column correctly to the output csv file, as writer quotes the column, so the result is "#CRHOM". This PR resolves this in a temporary solution, by removing the hash, that will be readded before the vep command is executed in the orchestration.

🛠 What does this PR implement

🙈 Missing

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@github-actions github-actions bot added bug Something isn't working size-S Step labels Nov 4, 2024
@project-defiant project-defiant marked this pull request as ready for review November 4, 2024 16:30
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@DSuveges DSuveges left a comment

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All makes sense!

@DSuveges DSuveges merged commit 4d8e7c4 into dev Nov 5, 2024
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@DSuveges DSuveges deleted the chr-quotes branch November 5, 2024 13:39
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2 participants