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Add gitpod and mamba profiles to the pipeline template#1673

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mahesh-panchal merged 2 commits into
nf-core:devfrom
mahesh-panchal:dev
Jul 14, 2022
Merged

Add gitpod and mamba profiles to the pipeline template#1673
mahesh-panchal merged 2 commits into
nf-core:devfrom
mahesh-panchal:dev

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@mahesh-panchal

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Adds profiles for gitpod and mamba to the pipeline template.
Gitpod requires a few additional settings in order to make full use of the resources for workflow testing.
Mamba is increasingly used over conda, and so it makes sense to have a profile for it.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@matthdsm matthdsm left a comment

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I like it!

@maxulysse

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I like this idea

@codecov

codecov Bot commented Jul 14, 2022

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Codecov Report

Merging #1673 (cacb9b2) into dev (77f43e8) will decrease coverage by 0.00%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev    #1673      +/-   ##
==========================================
- Coverage   68.07%   68.07%   -0.01%     
==========================================
  Files          56       56              
  Lines        6588     6587       -1     
==========================================
- Hits         4485     4484       -1     
  Misses       2103     2103              
Impacted Files Coverage Δ
nf_core/modules/remove.py 80.00% <0.00%> (-0.56%) ⬇️

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@jfy133 jfy133 left a comment

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LGTM, both would be useful. Is there docs confirming the size of a gitpod node? 60.GB seems quite large for a ('free'-service!)

@mahesh-panchal

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There's no docs. It can change at any time to be honest. I use htop to check memory and cpus available

@mahesh-panchal mahesh-panchal merged commit 2763932 into nf-core:dev Jul 14, 2022
@mahesh-panchal mahesh-panchal deleted the dev branch July 14, 2022 09:14
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4 participants