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Update controlfreec version #1241

Merged
merged 2 commits into from
Sep 18, 2023
Merged

Update controlfreec version #1241

merged 2 commits into from
Sep 18, 2023

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FriederikeHanssen
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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 - 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 --outdir <OUTDIR>).
  • 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).

@maxulysse
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Why patching the makegraph modules?
How do we deal with ploidy?

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github-actions bot commented Sep 18, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6242c31

+| ✅ 141 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-18 07:39:09

@FriederikeHanssen
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FriederikeHanssen commented Sep 18, 2023 •
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Currently in the args:

sarek/conf/modules/controlfreec.config

Line 54 in 1a263a2

ext.args = { "${params.cf_ploidy}" }

the problem is mutliple ploidy values which I attempt to fix here #980 but it's tricky. Patching to keep previous behavoir. Makegraph2 seems to fix it. I haven't time to test it yet. I would rather put my effort into getting makegraph2 to run then fixing this here now.

@maxulysse maxulysse merged commit d50e63b into nf-core:dev Sep 18, 2023
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse