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Implement unified quantification #85

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wants to merge 21 commits into from
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Implement unified quantification #85

wants to merge 21 commits into from

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nictru
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@nictru nictru commented Nov 21, 2023

Since splice junction count values can not reliably be compared across detection methods, I added PSIRC in order to re-quantify the circRNAs based on the BSJs detected by the various detection methods.

@nictru nictru self-assigned this Nov 21, 2023
@nictru nictru added the enhancement Improvement for existing functionality label Nov 21, 2023
rreggiar
rreggiar reviewed Nov 27, 2023
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Yeah so in my fork I did this by line instead of chromosome ... any reason that's your choice here? Interested in the motivation, speed? something about psirc?

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Also, why do we only want to annotated the combined circRNAs? I think having annotations for tool-specific circles could prove quite useful

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nictru commented Nov 29, 2023

Hey, the comments you made should be discussed in #84, gonna answer there

@nictru nictru mentioned this pull request Nov 29, 2023
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github-actions bot commented Jan 12, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 5d937da

+| ✅ 156 tests passed       |+
!| ❗   3 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/circrna/tree/dev" target="_blank">nf-core/circrna</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/circrna/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/circrna/releases/tag/dev" target="_blank">nf-core/circrna</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/circrna/dev/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • system_exit - System.exit in circrna.nf: System.exit(1) [line 43]

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-13 14:23:32

@nictru nictru closed this Mar 18, 2024
@nictru nictru deleted the quantification branch March 18, 2024 17:54
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