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Fix duplicate substrings in tools and skip_tools #641

Merged
merged 10 commits into from
Jul 17, 2022
Merged

Fix duplicate substrings in tools and skip_tools #641

merged 10 commits into from
Jul 17, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Jul 16, 2022 •
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PR checklist

  • 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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 16, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 211e62d

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-17 10:13:35

@maxulysse
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do we really need to add this split on tools?

@FriederikeHanssen
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FriederikeHanssen commented Jul 17, 2022 •
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do we really need to add this split on tools?

as far as I see it yes.

params.tools is a string -> .split(',') turns it into a list, new elements are detected by , -> then markduplicates and markduplicates_report are separate entries and can't both be detected by the same query.

Or alternatively we could rename the values so they don't share substrings

@maxulysse
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do we really need to add this split on tools?

as far as I see it yes.

params.tools is a string -> .split(',') turns it into a list, new elements are detected by , -> then markduplicates and markduplicates_report are separate entries and can't both be detected by the same query

Now I see, but we would need that only when we need to differentiate between markduplicates and markduplicates_report, not for any others?

@FriederikeHanssen
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Now I see, but we would need that only when we need to differentiate between markduplicates and markduplicates_report, not for any others?

that is right, also for baserecalibrator . The rest I did more to have it the same way everywhere. But happy to reverse it.

@maxulysse
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No, it's fine, better be safe than sorry.

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review July 17, 2022 10:20
@maxulysse maxulysse merged commit 28aa979 into nf-core:dev Jul 17, 2022
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@FriederikeHanssen @maxulysse