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Module: ichorcna/run updated to v0.5.0 #2767

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wants to merge 15 commits into from
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Module: ichorcna/run updated to v0.5.0 #2767

wants to merge 15 commits into from

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adamrtalbot
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@adamrtalbot adamrtalbot commented Jan 23, 2023 •
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Changes:

  • ichorcna no longer has a CLI, so it has been updated to use native R
  • Some additional parameters have been added
  • Requires scStates option in nextflow.config or it crashes

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

Module: ichorcna/run updated to v0.5.0
6f2ed6c 
Changes:
 - ichorcna no longer has a CLI, so it has been updated to use native R
 - Some additional parameters have been added
 - Requires scStates option in nextflow.config or it crashes
@adamrtalbot
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@nf-core-bot fix linting

@SPPearce
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SPPearce commented Feb 1, 2023

Looks generally good, few minor points.
Is the meta.yml not updated? Presumably that still points at the old broad institute github link.

SPPearce
SPPearce reviewed Feb 1, 2023
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modules/nf-core/ichorcna/run/main.nf Outdated Show resolved Hide resolved
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tests/modules/nf-core/ichorcna/run/main.nf Outdated Show resolved Hide resolved
modules/nf-core/ichorcna/run/main.nf Outdated

input:
tuple val(meta), path(wig)
path gc_wig
path map_wig
path panel_of_normals
path normal_wig
path normal_rds
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Not sold on normal_rds as the name of this.

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It's not great, but I'm not sure what else to call it. I need something to distinguish it from a wig file...normal_background?

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@nf-core-bot fix linting

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github-actions bot commented Mar 7, 2023

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

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@nf-core-bot fix linting

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SPPearce commented Oct 2, 2023

Hey @adamrtalbot , shall we get this finished off and merged in?

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Hey @adamrtalbot , shall we get this finished off and merged in?

What do we need to do? I need a ✅ review to get this merged.

@adamrtalbot adamrtalbot requested a review from a team as a code owner December 6, 2023 13:57
@adamrtalbot adamrtalbot requested review from edmundmiller and removed request for a team December 6, 2023 13:57
@edmundmiller edmundmiller added the stale Stale label Feb 19, 2024
edmundmiller
edmundmiller approved these changes Jun 28, 2024
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I'll bite. Last Review reminder in Slack for me 😬

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I have a half-done conversion to nf-test actually

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SPPearce commented Aug 6, 2024

Superceded by #6079 as I couldn't edit Adam's branch.

@SPPearce SPPearce closed this Aug 6, 2024
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