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use s3 path for pipeline test data#248

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maxulysse merged 2 commits intonf-core:devfrom
maxulysse:test_data_pipeline_s3
Jan 12, 2024
Merged

use s3 path for pipeline test data#248
maxulysse merged 2 commits intonf-core:devfrom
maxulysse:test_data_pipeline_s3

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@maxulysse maxulysse commented Jan 11, 2024

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/fetchngs 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>).
  • 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).

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github-actions bot commented Jan 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 84adb51

+| ✅ 136 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-12 15:52:21

adamrtalbot
adamrtalbot requested changes Jan 12, 2024
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Changelog please!

@maxulysse maxulysse marked this pull request as ready for review January 12, 2024 15:51
@maxulysse maxulysse requested a review from adamrtalbot January 12, 2024 15:54
@maxulysse maxulysse merged commit ea0a0a3 into nf-core:dev Jan 12, 2024
@maxulysse maxulysse deleted the test_data_pipeline_s3 branch January 16, 2024 13:38
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