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Add flag to only output BAM files #213

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alkc
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@alkc alkc commented Jul 29, 2024 •
edited by Jakob37
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Description and reviewer info

This update adds a flag --alignment_only to instruct the pipeline to only output BAMs and QC data.

Will be used to regenerate BAM files for /access/wgs/bam and whambam.

Type of change

  • Minor change

Checklist

  • Self-review of my code
  • Update the CHANGELOG
  • Tag the latest commit (vX.Y.Z format)
  • Log samples used for testing in the Verification_samples_log Excel sheet

Specific tests

  • Bam + QC only run for onco works
  • Bam + QC only run for wgs works

Major / Minor change

  • Stub run completes without errors or new warnings
  • onco run finishes without any new warnings/errors and the results can
    be loaded into scout
  • wgs single run finishes without any new warnings/errors and the results
    can be loaded into scout
  • wgs trio run finishes without any new warnings/errors and the results
    can be loaded into scout
  • At least one other person has reviewed and approved my code
  • I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

(Add if missing)

Testing performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

@alkc alkc linked an issue Jul 29, 2024 that may be closed by this pull request
Add flag to stop pipeline when bam + qc has been generated #212
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@alkc alkc added the enhancement New feature or request label Jul 29, 2024
Jakob37
Jakob37 approved these changes Aug 15, 2024
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@Jakob37 Jakob37 left a comment •
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Looks good!

Have you checked the trace file diff from stub runs to make sure you get the expected behavious for all profiles? (Guess you might have, just double checking).

@Jakob37 Jakob37 mentioned this pull request Aug 22, 2024
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alkc commented Sep 6, 2024

Put on hold while I deal with the reruns, but what I'd like to do next is to test run this a final time after merging master into this branch, then it should be ready to merge and deploy

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alkc commented Oct 7, 2024 •
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[...] but what I'd like to do next is to test run this a final time after merging master into this branch, then it should be ready to merge and deploy

Thank you for noting this down, self from the past.

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Add flag to stop pipeline when bam + qc has been generated
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