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Created subworkflow for parsing samplesheet with nf-test #1286

Merged
merged 5 commits into from
Oct 18, 2023
Merged

Created subworkflow for parsing samplesheet with nf-test #1286

merged 5 commits into from
Oct 18, 2023

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RaqManzano
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Generated a new subworkflow for parsing samplesheet with its corresponding nf-test.

@RaqManzano RaqManzano added the enhancement New feature or request label Oct 16, 2023
@RaqManzano RaqManzano self-assigned this Oct 16, 2023
@RaqManzano RaqManzano requested a review from maxulysse as a code owner October 16, 2023 13:23
@RaqManzano RaqManzano mentioned this pull request Oct 16, 2023
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@RaqManzano
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Fixes #1285

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github-actions bot commented Oct 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8c7d04e

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 07:52:03

FriederikeHanssen
FriederikeHanssen reviewed Oct 16, 2023
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looks great ! Thank you so much 🙏 just testing it quickly on the cluster, always scared when we change the sample sheet parsing :D

maxulysse
maxulysse reviewed Oct 16, 2023
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subworkflows/local/samplesheet_to_channel/main.nf.test Outdated
Comment on lines 20 to 21
file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz'),
file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz'),
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if we use test_cache profile, then we can use the map from https://github.com/nf-core/test-datasets/blob/sarek3/tests/config/test_data.config

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Looking amazingly good, we'd just need to add nf-test in the .github/workflows/ci.yml.

@adamrtalbot any idea to make it work while we still have pytest tests with tags.yml?

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Needs https://github.com/nf-core/sarek/pull/1289/checks

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@maxulysse @RaqManzano could one of you update from dev? I don't seem to be able to. Not sure why not.

adamrtalbot
adamrtalbot reviewed Oct 18, 2023
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nf-test.config Outdated Show resolved Hide resolved
@adamrtalbot @FriederikeHanssen
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8c7d04e 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
FriederikeHanssen
FriederikeHanssen approved these changes Oct 18, 2023
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❤️

@RaqManzano RaqManzano merged commit e268850 into nf-core:dev Oct 18, 2023
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@adamrtalbot adamrtalbot adamrtalbot left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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enhancement New feature or request
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Hackathon: November 2023
Status: Done
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@RaqManzano @maxulysse @adamrtalbot @FriederikeHanssen