ci: Remove Nextflow caching #1202

edmundmiller · 2023-08-31T13:44:43Z

Also, just uses the latest release of setup-nextflow.

nf-core/setup-nextflow#19

subworkflows/local/bam_markduplicates/main.nf

maxulysse · 2023-08-31T13:47:14Z

Looking good, can you update CHANGELOG

github-actions · 2023-08-31T13:47:26Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 83b2647

+| ✅ 149 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.3.0
schema_lint - Input mimetype is missing or empty
schema_description - No description provided in schema for parameter: input_restart

❔ Tests ignored:

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
template_strings - template_strings
schema_params - schema_params
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowSarek.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-sarek_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: pytest-workflow_release.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-08-31 14:17:45

edmundmiller · 2023-08-31T13:54:03Z

My take, we merge this and see if it makes it better or worse, then we'll know if it's setup-nextflow or not. I'm guessing it's all the caching that's going on with the test data as well...

We can also try directly passing the token. nf-core/setup-nextflow#21

maxulysse · 2023-08-31T13:55:34Z

I don't think it's working as we would want it to work

edmundmiller · 2023-08-31T14:17:03Z

I guess we won't know until we try.

maxulysse · 2023-08-31T14:18:13Z

I guess we won't know until we try.

Fire away then

ci: Remove Nextflow caching

f82478d

nf-core/setup-nextflow#19

edmundmiller added the testing label Aug 31, 2023

edmundmiller requested a review from maxulysse as a code owner August 31, 2023 13:44

edmundmiller self-assigned this Aug 31, 2023

maxulysse reviewed Aug 31, 2023

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subworkflows/local/bam_markduplicates/main.nf Outdated Show resolved Hide resolved

edmundmiller force-pushed the setup-nextflow branch from 7f750b6 to eef68ca Compare August 31, 2023 13:53

edmundmiller added 3 commits August 31, 2023 09:15

ci: Use latest wretry action

74a1fb7

ci: Update setup-python to v4

43cefc6

chore: Update CHANGELOG

83b2647

edmundmiller force-pushed the setup-nextflow branch from 928cb2a to 83b2647 Compare August 31, 2023 14:15

maxulysse approved these changes Aug 31, 2023

View reviewed changes

edmundmiller merged commit 159f0e3 into nf-core:dev Aug 31, 2023
8 checks passed

edmundmiller deleted the setup-nextflow branch August 31, 2023 14:22

adamrtalbot mentioned this pull request Aug 31, 2023

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ci: Remove Nextflow caching #1202

ci: Remove Nextflow caching #1202

edmundmiller commented Aug 31, 2023

maxulysse commented Aug 31, 2023

github-actions bot commented Aug 31, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Aug 31, 2023 •

edited

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maxulysse commented Aug 31, 2023

edmundmiller commented Aug 31, 2023

maxulysse commented Aug 31, 2023

ci: Remove Nextflow caching #1202

ci: Remove Nextflow caching #1202

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edmundmiller commented Aug 31, 2023

maxulysse commented Aug 31, 2023

github-actions bot commented Aug 31, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Aug 31, 2023 • edited Loading

maxulysse commented Aug 31, 2023

edmundmiller commented Aug 31, 2023

maxulysse commented Aug 31, 2023

github-actions bot commented Aug 31, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️

edmundmiller commented Aug 31, 2023 •

edited

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