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only check pipeline name without dashes if the name is provided by prompt #2123

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merged 5 commits into from
Dec 13, 2022

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mirpedrol
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@mirpedrol mirpedrol commented Dec 12, 2022

Related to #2117 and slack discussion

The code will check that the pipeline name doesn't contain dashes if the name if provided by prompt. With nf-core create or nf-core create --name my-name.
It won't be checked if the pipeline name is provided with a template nf-core create -t template.yml where template.yml contains:

name: my-name
description: A test pipeline
author: me
prefix: my-org

If template.yml doesn't provide a custom prefix or the prefix is set to nf-core, dashes won't be allowed.

To sync a pipeline created with dashes, the template must be used: nf-core sync -t template.yml

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

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codecov bot commented Dec 12, 2022

Codecov Report

Merging #2123 (d97e116) into dev (bc44d2e) will decrease coverage by 0.00%.
The diff coverage is 40.00%.

❗ Current head d97e116 differs from pull request most recent head 5ccbae8. Consider uploading reports for the commit 5ccbae8 to get more accurate results

@@            Coverage Diff             @@
##              dev    #2123      +/-   ##
==========================================
- Coverage   71.42%   71.41%   -0.01%     
==========================================
  Files          77       77              
  Lines        8356     8358       +2     
==========================================
+ Hits         5968     5969       +1     
- Misses       2388     2389       +1     
Impacted Files Coverage Δ
nf_core/sync.py 75.10% <0.00%> (-0.32%) ⬇️
nf_core/create.py 65.01% <66.66%> (+0.13%) ⬆️

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@mirpedrol
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@nvnieuwk would be good if you could test this with your pipeline 🙂

@nvnieuwk
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It seems to work!

$ nf-core sync -t template.yml

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.8.dev0 - https://nf-co.re


INFO     Pipeline directory: /home/nvnieuwk/Documents/cmgg/nf-cmgg-germline                                                                                 
INFO     Original pipeline repository branch is 'restructure-genotyping'                                                                                    
INFO     Deleting all files in 'TEMPLATE' branch                                                                                                            
INFO     Making a new template pipeline using pipeline variables                                                                                            
INFO     Committed changes to 'TEMPLATE' branch                                                                                                             
INFO     Checking out original branch: 'restructure-genotyping'                                                                                             
INFO     Now try to merge the updates in to your pipeline:                                                                                                  
           cd /home/nvnieuwk/Documents/cmgg/nf-cmgg-germline                                                                                                
           git merge TEMPLATE 

@ewels ewels merged commit ed9cbb4 into nf-core:dev Dec 13, 2022
@mirpedrol mirpedrol deleted the dashed-name branch December 13, 2022 15:48
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4 participants