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Sentieon dedup #3224

Merged
merged 34 commits into from
Mar 30, 2023
Merged

Sentieon dedup #3224

merged 34 commits into from
Mar 30, 2023

Commits on Mar 30, 2023

  1. Fixing stub

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    asp8200 committed Mar 30, 2023
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  2. Adding Sentieon-Dedup module and test

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    asp8200 committed Mar 30, 2023
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  3. Skipping conda for all tests tagged sentieon

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    asp8200 committed Mar 30, 2023
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  4. Adding test for sentieon-dedup

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    asp8200 committed Mar 30, 2023
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  5. Not running conda test for sentieon modules

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    asp8200 committed Mar 30, 2023
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  6. WIP: Trying to hardcode output to cram

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    asp8200 committed Mar 30, 2023
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  7. Fixing suffix

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    asp8200 committed Mar 30, 2023
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  8. WIP: Fetch md5sums

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    asp8200 committed Mar 30, 2023
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  9. Updating md5sums

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    asp8200 committed Mar 30, 2023
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  10. Removing outdated comments

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    asp8200 committed Mar 30, 2023
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  11. Adding extra args for driver, LocusCollector and Dedup

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    asp8200 committed Mar 30, 2023
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  12. yml-doc for Dedup-module

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    asp8200 committed Mar 30, 2023
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  13. Adding updating for rmdup in test-config

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  14. WIP: Adding test for dedup rmdup

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  15. Removing unwanted tags

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    asp8200 committed Mar 30, 2023
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  16. Trying to run two dedup-tests

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  17. Adding test of sentieon dedup with removal of reads

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    asp8200 committed Mar 30, 2023
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  18. Re-adding secrets

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    asp8200 committed Mar 30, 2023
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  19. Removing option rmdup from test yaml

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  20. Update tests/modules/nf-core/sentieon/dedup/nextflow.config 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  21. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  22. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  23. Update modules/nf-core/sentieon/bwamem/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  24. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  25. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  26. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  27. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  28. Update modules/nf-core/sentieon/dedup/main.nf 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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    asp8200 and maxulysse committed Mar 30, 2023
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  29. Adding prefix for stub

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    asp8200 committed Mar 30, 2023
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  30. fix

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    asp8200 committed Mar 30, 2023
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  31. fix

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    asp8200 committed Mar 30, 2023
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  32. fix

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    asp8200 committed Mar 30, 2023
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  33. Updating md5sums

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    asp8200 committed Mar 30, 2023
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  34. Merge branch 'master' into sentieon_dedup

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    asp8200 committed Mar 30, 2023
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