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Create nf-tests for create_annotated_tables module #103

Merged
merged 17 commits into from
Nov 22, 2024
Merged

Create nf-tests for create_annotated_tables module #103

merged 17 commits into from
Nov 22, 2024

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alanmmobbs93
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@alanmmobbs93 alanmmobbs93 commented Nov 21, 2024 •
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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/nanostring branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

Reported issues

Changes

Update module structure to nf-core standards

  • Create environment.yml for conda.
  • Add stub block
  • Update containers to seqera containers

Add nf-tests for module.

  • Create snapashot
  • Update pipeline snapshots.

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github-actions bot commented Nov 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c1eaaa2

+| ✅ 199 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-22 14:41:10

@alanmmobbs93 alanmmobbs93 mentioned this pull request Nov 21, 2024
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atrigila
atrigila reviewed Nov 22, 2024
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workflows/nanostring.nf
@@ -91,7 +91,7 @@ workflow NANOSTRING {
// MODULE: Annotate normalized counts with metadata from the samplesheet
//
CREATE_ANNOTATED_TABLES (
NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK),
NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK).toSortedList().flatten(),
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Well done! :)

nschcolnicov
nschcolnicov reviewed Nov 22, 2024
View reviewed changes
modules/local/nacho/normalize/tests/main.nf.test.snap Outdated
@@ -9,7 +9,7 @@
"normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
],
"2": [
"versions.yml:md5,0b8556f7dd763f21894470ecc737ca3b"
"versions.yml:md5,dd0bb0b151596e1316c29a51f38f5a2e"
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@alanmmobbs93 Why was this snap updated?

@alanmmobbs93 alanmmobbs93 merged commit c20d880 into nf-core:dev Nov 22, 2024
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@atrigila atrigila atrigila left review comments

@nschcolnicov nschcolnicov nschcolnicov approved these changes

@apeltzer apeltzer apeltzer approved these changes

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4 participants
@alanmmobbs93 @apeltzer @atrigila @nschcolnicov