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Add map to full test#280

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LouisLeNezet wants to merge 1 commit intonf-core:devfrom
LouisLeNezet:add_map_full_test
Open

Add map to full test#280
LouisLeNezet wants to merge 1 commit intonf-core:devfrom
LouisLeNezet:add_map_full_test

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@LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Mar 31, 2026

I did not found a better resources for genetic map file by chromosomes.

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/phaseimpute branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@LouisLeNezet LouisLeNezet self-assigned this Mar 31, 2026
@LouisLeNezet LouisLeNezet requested a review from atrigila March 31, 2026 11:21
@atrigila
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atrigila commented Apr 3, 2026

We are not sure this works, right? Can we trigger a 'test' in Seqera Cloud by attempting to push to master?

Also, I have been thinking lately that the test full should test all 4 tools. Let me know your thoughts.

@LouisLeNezet
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We are not sure this works, right? Can we trigger a 'test' in Seqera Cloud by attempting to push to master?

This should works, but I didn't check. If an error is present we will see it with the PR to main indeed.

Also, I have been thinking lately that the test full should test all 4 tools. Let me know your thoughts.

The only issue, is that it will increase by quite a lot the computational time and therefore the cost of the test.
I do not know by how much, nor how much it would be accepted.

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