Fresh CI #227

edmundmiller · 2024-08-06T18:38:49Z

Uses the new CI from the nf-test tutorial

ci mode
Filter based on pipeline,workflow
Only run tests on files that have been changed in the PR
Splits up the tests automatically

github-actions · 2024-08-06T18:40:10Z

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

Posted for pipeline commit 1b72fbb

+| ✅ 191 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
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
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
actions_ci - actions_ci

✅ 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: 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-demultiplex_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-demultiplex_logo_light.png
files_exist - File found: docs/images/nf-core-demultiplex_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: 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: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-demultiplex_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowDemultiplex.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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 manifest.version ends in dev: 1.5.0dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.trim_fastq= true
nextflow_config - Config default value correct: params.skip_tools= []
nextflow_config - Config default value correct: params.sample_size= 100000
nextflow_config - Config default value correct: params.downstream_pipeline= default
nextflow_config - Config default value correct: params.demultiplexer= bclconvert
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.checkqc_config= []
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.remove_adapter= true
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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 - 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 - assets/nf-core-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
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_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (252 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - BCLCONVERT found in conf/modules.config and Nextflow scripts.
modules_config - BCL2FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - BASES2FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - MD5SUM found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - SGDEMUX found in conf/modules.config and Nextflow scripts.
modules_config - FQTK found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKFASTQ found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - CHECKQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-08-12 18:57:05

https://www.nf-test.com/tutorials/github-actions/

.github/workflows/ci.yml

Remove redundant pipeline tag

This reverts commit c44e7c8.

edmundmiller · 2024-08-12T18:31:35Z

LGTM!

Is it necessary to have both the configs and profile?

atrigila · 2024-08-12T18:34:06Z

LGTM!

Is it necessary to have both the configs and profile?

I was working on that! :)

edmundmiller changed the base branch from master to dev August 6, 2024 18:39

nf-core deleted a comment from github-actions bot Aug 6, 2024

edmundmiller force-pushed the fresh-ci branch from 01a12e6 to 3eff227 Compare August 6, 2024 18:40

apeltzer mentioned this pull request Aug 8, 2024

Improve nf-tests #232

Closed

4 tasks

edmundmiller force-pushed the fresh-ci branch from d186b5f to 0701aa9 Compare August 8, 2024 23:20

edmundmiller self-assigned this Aug 8, 2024

edmundmiller added 5 commits August 8, 2024 18:27

ci: Try using new CI from official nf-test tutorial

62953f3

https://www.nf-test.com/tutorials/github-actions/

ci: Only test pipeline and subworkflows for now

a368bfe

style: Make it more readable

3fbf3bb

fixup! subworkflows => workflows

4f4cbd5

ci: Actually use the nf-test version

6a68043

edmundmiller force-pushed the fresh-ci branch from 0701aa9 to 35dd615 Compare August 8, 2024 23:29

ci: Define total shards to avoid version issues

af488b0

edmundmiller force-pushed the fresh-ci branch from 35dd615 to af488b0 Compare August 9, 2024 00:55

ci: Use setup-nf-test

3a03356

edmundmiller marked this pull request as ready for review August 9, 2024 01:03

edmundmiller requested review from a team and Aratz and removed request for a team August 9, 2024 01:07

edmundmiller added this to the 1.5.0 milestone Aug 9, 2024

apeltzer approved these changes Aug 9, 2024

View reviewed changes

nschcolnicov reviewed Aug 9, 2024

View reviewed changes

.github/workflows/ci.yml Show resolved Hide resolved

.github/workflows/ci.yml Show resolved Hide resolved

nschcolnicov and others added 4 commits August 9, 2024 15:43

Added resource definitions to nf-tests

1ea4a7f

test: Add explicit config

6f3abdb

Remove redundant pipeline tag

Associated configs to nftests

e84f14d

remove publishdir from config

c44e7c8

atrigila requested a review from a team as a code owner August 12, 2024 13:23

atrigila added 2 commits August 12, 2024 15:32

Revert "remove publishdir from config"

d51c4d4

This reverts commit c44e7c8.

update nf-tests with profile

761d273

fix bclconvert test

d69dbbc

atrigila self-assigned this Aug 12, 2024

atrigila added 2 commits August 12, 2024 16:30

renamed test workflows for better CI traceability

ab49b06

change config for profile

2c9a8eb

Merge branch 'dev' into fresh-ci

da4c627

remove redundant params

1b72fbb

atrigila merged commit 0381e51 into dev Aug 12, 2024
10 checks passed

apeltzer deleted the fresh-ci branch August 12, 2024 19:47

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fresh CI #227

Fresh CI #227

edmundmiller commented Aug 6, 2024 •

edited

Loading

github-actions bot commented Aug 6, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Aug 12, 2024

atrigila commented Aug 12, 2024

Fresh CI #227

Fresh CI #227

Conversation

edmundmiller commented Aug 6, 2024 • edited Loading

github-actions bot commented Aug 6, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Aug 12, 2024

atrigila commented Aug 12, 2024

edmundmiller commented Aug 6, 2024 •

edited

Loading

github-actions bot commented Aug 6, 2024 •

edited

Loading

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