template - basic pipeline level nf-test tests #3469

maxulysse · 2025-02-26T13:04:32Z

Related updated docs: nf-core/website#3216

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

CHANGELOG.md

mashehu

we should not merge this without a corresponding PR with docs

maxulysse · 2025-02-26T13:18:27Z

we should not merge this without a corresponding PR with docs

That's on the way

maxulysse · 2025-02-26T13:30:16Z

Thinking that people might not want to use nf-test, so we should have a flag for this.
And then have in the linting either ci.yml or nf-test.yml, but not both as the default test should be -profile test

nf_core/pipeline-template/.github/workflows/nf-test.yml

nf_core/pipeline-template/nf-test.config

nf_core/pipeline-template/tests/.nftignore

docs PR is available

nf_core/pipeline-template/.github/workflows/nf-test.yml

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

nf_core/pipeline-template/.github/actions/nf-test/action.yml

nf_core/pipeline-template/.github/workflows/nf-test.yml

nf_core/pipeline-template/tests/.nftignore

nf_core/pipeline-template/tests/nextflow.config

nf_core/pipelines/create/template_features.yml

mirpedrol · 2025-02-27T11:42:40Z

nf_core/pipelines/create/template_features.yml

@@ -401,7 +403,9 @@ test_config:
    - "conf/test_full.config"
    - ".github/workflows/awsfulltest.yml"
    - ".github/workflows/awstest.yml"
-    - ".github/workflows/ci.yml"
+    - ".github/workflows/nf-test.yml"


when skipping tests, we should also skip nf-test.config and the tests directory

mirpedrol · 2025-02-27T11:42:56Z

nf_core/pipelines/create/template_features.yml

@@ -416,7 +420,9 @@ test_config:
    files_exist:
      - "conf/test.config"
      - "conf/test_full.config"
-      - ".github/workflows/ci.yml"
+      - ".github/workflows/nf-test.yml"


skip nf-test files

mirpedrol · 2025-02-27T11:43:46Z

nf_core/pipelines/lint/files_exist.py

-        .github/workflows/ci.yml
+        .github/workflows/nf-test.yml
+        .github/actions/get-shards/action.yml
+        .github/actions/nf-test/action.yml


We should also lint for nf-test files

mirpedrol · 2025-02-27T11:52:35Z

Thinking that people might not want to use nf-test, so we should have a flag for this.
And then have in the linting either ci.yml or nf-test.yml, but not both as the default test should be -profile test

I would say if we move to nf-test that should be the only way to test. There could be an option to skip testing, but if you test, it has to be with nf-test

mashehu · 2025-02-27T11:54:36Z

💯 i guess the difference to before is now that nf-test adds some files to the template and given some people want a very bare-bone structure, we should probably have a skip feature.

maxulysse · 2025-02-28T09:26:23Z

Needs some more improvments, I'm trying it out in nf-core/rnavar#178, which uncovers some issue I didn't find in sarek.
sorry about that

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

maxulysse · 2025-03-03T09:50:18Z

also update link to badge in README

nf_core/pipeline-template/nf-test.config

nf_core/pipeline-template/.github/workflows/nf-test.yml

maxulysse · 2025-03-18T15:33:39Z

nf_core/pipeline-template/.github/workflows/nf-test.yml

+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMain:
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}


we can think of updating this test when we fully remove master

nf_core/pipeline-template/tests/nextflow.config

mirpedrol

only one last comment, otherwise LGTM 🚀

nf_core/pipeline-template/.github/workflows/nf-test.yml

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

mirpedrol · 2025-03-20T12:05:26Z

I can take care of fixing the failing test and then merging 👍

add a feature to skip nf-test for custom pipelines

…ipeline

codecov · 2025-03-21T11:25:54Z

Codecov Report

Attention: Patch coverage is 88.88889% with 1 line in your changes missing coverage. Please review.

Project coverage is 76.87%. Comparing base (96097ac) to head (35befd4).
Report is 35 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/pipelines/lint/actions_nf_test.py	88.88%	1 Missing ⚠️

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maxulysse and others added 2 commits February 26, 2025 14:03

basic nf-test skeleton

5f6ff91

[automated] Update CHANGELOG.md

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maxulysse commented Feb 26, 2025

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maxulysse and others added 2 commits February 26, 2025 14:06

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config files

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mashehu previously requested changes Feb 26, 2025

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maxulysse requested a review from mashehu February 26, 2025 14:42

mashehu reviewed Feb 27, 2025

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update linting for new ci

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use new file structure

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mashehu reviewed Feb 27, 2025

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mashehu and others added 5 commits February 27, 2025 11:03

fix naming

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Apply suggestions from code review

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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

fix typo

303a960

update api docs structure

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fix key error

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mirpedrol reviewed Feb 27, 2025

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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

mashehu marked this pull request as draft February 28, 2025 19:46

maxulysse commented Mar 4, 2025

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maxulysse and others added 3 commits March 4, 2025 11:35

Apply suggestions from code review

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Merge branch 'dev' into nf-test-pipeline

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Update action.yml

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maxulysse and others added 3 commits March 13, 2025 13:19

Update nf_core/pipeline-template/nf-test.config

ee1f13b

Apply suggestions from code review

891b191

clean up

be0c717

maxulysse commented Mar 18, 2025

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Update nf_core/pipeline-template/.github/workflows/nf-test.yml

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maxulysse commented Mar 18, 2025

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Update nf_core/pipeline-template/.github/workflows/nf-test.yml

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maxulysse commented Mar 18, 2025

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Update nf_core/pipeline-template/tests/nextflow.config

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mirpedrol approved these changes Mar 18, 2025

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maxulysse and others added 2 commits March 20, 2025 12:58

Merge branch 'dev' into nf-test-pipeline

e9807b3

Update nf_core/pipeline-template/.github/workflows/nf-test.yml

151002b

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

maxulysse marked this pull request as ready for review March 20, 2025 12:00

add a feature to skip nf-test for custom pipelines

1af13fe

mirpedrol mentioned this pull request Mar 21, 2025

add a feature to skip nf-test for custom pipelines maxulysse/nf-core_tools#2

Merged

maxulysse and others added 7 commits March 21, 2025 10:56

Merge pull request #2 from mirpedrol/pr_3469

1392bad

add a feature to skip nf-test for custom pipelines

format with pre-commit

840d569

fix jinja template and ignore more nf-test files

95d437a

fix jinja again - sorry

c37d3ef

update custom pipeline textual snapshot

1b9774f

Merge branch 'dev' of https://github.com/nf-core/tools into nf-test-p…

0197999

…ipeline

update more textual snapshots

7c4b606

mirpedrol mentioned this pull request Mar 21, 2025

Tools pipeline tests use nf-test #3497

Closed

mirpedrol added 2 commits March 21, 2025 11:31

lint tests/default.nf.test and nf-test.config files exist

fc22579

update docs in contributing.md

35befd4

mirpedrol enabled auto-merge March 21, 2025 11:54

mirpedrol merged commit e872751 into nf-core:dev Mar 21, 2025
94 checks passed

mirpedrol mentioned this pull request May 14, 2025

Lint for pipeline nf-test contents #3065

Closed

template - basic pipeline level nf-test tests #3469

template - basic pipeline level nf-test tests #3469

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