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Add validation step #22

Merged
merged 68 commits into from
Apr 24, 2024
Merged

Add validation step #22

merged 68 commits into from
Apr 24, 2024

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LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Mar 26, 2024 •
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  • Add the validation step.

  • Fix input channel depending on the step used

  • 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 lint).

  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).

  • 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 26, 2024
@LouisLeNezet LouisLeNezet added the enhancement New feature or request label Mar 26, 2024
@LouisLeNezet LouisLeNezet requested a review from atrigila March 26, 2024 09:17
atrigila
atrigila reviewed Mar 29, 2024
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@atrigila atrigila left a comment

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Good job, here are some initial suggestions for improvement!

modules/local/addcolumns/main.nf Show resolved Hide resolved
modules/local/concatenate/main.nf Outdated Show resolved Hide resolved
conf/test_validate.config Outdated Show resolved Hide resolved
conf/test_sim.config Outdated Show resolved Hide resolved
subworkflows/local/vcf_concordance_glimpse/main.nf Outdated Show resolved Hide resolved
conf/modules.config Outdated Show resolved Hide resolved
conf/test_validate.config Show resolved Hide resolved
subworkflows/local/vcf_concordance_glimpse/main.nf Outdated Show resolved Hide resolved
main.nf Outdated Show resolved Hide resolved
@LouisLeNezet LouisLeNezet linked an issue Apr 12, 2024 that may be closed by this pull request
modules.config should include the subworkflow #27
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@LouisLeNezet LouisLeNezet requested a review from atrigila April 23, 2024 17:29
@LouisLeNezet LouisLeNezet merged commit 411233e into nf-core:dev Apr 24, 2024
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@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Apr 24, 2024
@LouisLeNezet LouisLeNezet deleted the validation branch May 30, 2024 10:16
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@atrigila atrigila atrigila approved these changes

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@LouisLeNezet LouisLeNezet

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enhancement New feature or request
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modules.config should include the subworkflow
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@LouisLeNezet @atrigila