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Improving Sentieon-dedup-module #3315

Merged
merged 5 commits into from
Apr 24, 2023
Merged

Improving Sentieon-dedup-module #3315

merged 5 commits into from
Apr 24, 2023

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asp8200
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@asp8200 asp8200 commented Apr 24, 2023

Just enabling the user to set the name of the metrics file from dedup. That turned out to be useful when implementing the Sentieon-dedup-module in Sarek.

Not entirely sure why I had to update the md5sum for the cram-file in the test.yml just because the metrics file (content and name) was update. (The content of the metrics file is changed because it contains the command for generating the metrics file.)

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
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  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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@asp8200 asp8200 requested a review from maxulysse April 24, 2023 09:04
@asp8200 asp8200 changed the title DRAFT: Improving Sentieon-dedup-module Improving Sentieon-dedup-module Apr 24, 2023
@asp8200 asp8200 enabled auto-merge April 24, 2023 10:00
@asp8200 asp8200 added this pull request to the merge queue Apr 24, 2023
Merged via the queue into master with commit 8c04ecc Apr 24, 2023
@asp8200 asp8200 deleted the update_sentieon_dedup branch May 21, 2023 18:12
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2 participants