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Remove call to getGenomeAttribute in main.nf when running nf-core create without iGenomes #1674

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merged 3 commits into from
Jul 15, 2022

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ErikDanielsson
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The function call to getGenomesAttribute was not removed when running nf-core create without iGenomes, causing the pipeline to fail as was reported in #1670. This PR removes this function call.

I also removed references to the --genomes parameter when running nextflow <pipeline> --help in a pipeline without iGenomes, so it is displayed as

nextflow run fma/nftemplate --input samplesheet.csv -profile docker

rather than

nextflow run nf-core/testing --input samplesheet.csv --genome GRCh37 -profile docker

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

@ErikDanielsson ErikDanielsson linked an issue Jul 14, 2022 that may be closed by this pull request
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codecov bot commented Jul 14, 2022

Codecov Report

Merging #1674 (a354c2d) into dev (2763932) will decrease coverage by 0.01%.
The diff coverage is 38.46%.

@@            Coverage Diff             @@
##              dev    #1674      +/-   ##
==========================================
- Coverage   68.07%   68.06%   -0.02%     
==========================================
  Files          56       56              
  Lines        6588     6589       +1     
==========================================
  Hits         4485     4485              
- Misses       2103     2104       +1     
Impacted Files Coverage Δ
nf_core/__main__.py 52.35% <0.00%> (+0.01%) ⬆️
nf_core/create.py 62.65% <71.42%> (-0.36%) ⬇️

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LGTM!

@apeltzer apeltzer merged commit d5ee441 into nf-core:dev Jul 15, 2022
@ErikDanielsson ErikDanielsson deleted the fix-custom-create branch July 26, 2022 07:38
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nf-core template @dev errors
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