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Add pipeline-level nf-tests #14

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merged 3 commits into from
Nov 30, 2023
Merged

Add pipeline-level nf-tests #14

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690a71f
Add pipeline-level nf-tests
pinin4fjords Nov 29, 2023
56e255d
Remove non-nf-test covered by pipeline nf-test
pinin4fjords Nov 29, 2023
7bbb6e5
appease eclint
pinin4fjords Nov 29, 2023
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25 changes: 1 addition & 24 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,30 +17,6 @@ concurrency:

jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-aggregate dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'seqeralabs/nf-aggregate') }}"
runs-on: ubuntu-latest
env:
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
strategy:
matrix:
NXF_VER:
- "23.10.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

changes:
name: Check for changes
runs-on: ubuntu-latest
Expand Down Expand Up @@ -69,6 +45,7 @@ jobs:
fail-fast: false
matrix:
NXF_VER:
- "23.10.0"
- "latest-everything"
tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
profile:
Expand Down
23 changes: 23 additions & 0 deletions tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
nextflow_pipeline {

name "Test Workflow main.nf"
script "../main.nf"

tag "pipeline"
tag "pipeline_nf-aggregate"

test("Should run without failures") {

when {
params {
outdir = "results"
}
}

then {
assert workflow.success
}

}

}
5 changes: 5 additions & 0 deletions tests/tags.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
pipeline_nf-aggregate:
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Can we put this file in the workflows/nf_aggregate/ folder instead so everything is self-enclosed.

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So, these tests are referencing the main.nf in the root, so it's a pipeline-level one. I think we should probably have another one in the folder you indicate. At least nf-test docs reference both 'pipeline' and 'workflow' level tests, though I'm not sure what the value of both is.

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Ok. I'll move as required. Thanks!

- "**.nf"
- "**.config"
- "**.nf.test"
- "**.json"