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update resistance gene bed #46

Merged
merged 5 commits into from
Nov 5, 2024
Merged

update resistance gene bed #46

merged 5 commits into from
Nov 5, 2024

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taranewman
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@taranewman taranewman commented Oct 23, 2024

fixes #45 #47

do not merge until confirming jodyphelan/TBProfiler#398

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taranewman commented Oct 25, 2024

currently outputs ${sample_id}_tbprofiler_resistance_drug_coverage.csv, however this could be changed to output a different file name or replace ${sample_id}_tbprofiler_resistance.csv

github actions is failing, failed at first commit when updating resistance gene bed file, at tbprofiler step upstream of any effects of the changes

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@dfornika dfornika left a comment

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Looking good!

We'll investigate why the GitHub Actions test pipeline is failing later on. We've tested this on our local infrastructure, including with the same inputs as the test pipeline and it is running to completion successfully.

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I was going to wait to merge in case of any updates to formatting, but if needed will create another issue/ PR.

@taranewman taranewman merged commit 16a857d into main Nov 5, 2024
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Resistance genes bed file requires update
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