Initial PR getting tests to pass #1

mattheww95 · 2024-04-09T20:03:53Z

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github-actions · 2024-04-09T20:04:15Z

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github-actions · 2024-04-09T20:05:34Z

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

Posted for pipeline commit f83d634

+| ✅ 138 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.3
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/iridanextexample/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/iridanextexample/main/nextflow_schema.json
schema_description - No description provided in schema for parameter: av_html
schema_description - No description provided in schema for parameter: ar_config
schema_description - No description provided in schema for parameter: ar_thresholds
nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-iridanextexample_logo_light.png
files_exist - File is ignored: docs/images/nf-core-iridanextexample_logo_light.png
files_exist - File is ignored: docs/images/nf-core-iridanextexample_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowSnvphylnfc.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-iridanextexample_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-iridanextexample_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-iridanextexample_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/clustersplitter/clustersplitter/.github/workflows/awstest.yml
actions_awsfulltest - actions_awsfulltest
pipeline_name_conventions - pipeline_name_conventions

✅ 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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: 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-iridanextexample_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/Workflow.groovy
files_exist - File not found check: lib/WorkflowIridanextexample.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.av_html= assets/ArborView.html
nextflow_config - Config default value correct: params.ar_config= tests/data/configs/config.json
nextflow_config - Config default value correct: params.ar_thresholds= 10,9,8,7,6,5,4,3,2,1
nextflow_config - Config default value correct: params.project_name= assembly
nextflow_config - Config default value correct: params.assembler= stub
nextflow_config - Config default value correct: params.random_seed= 1
nextflow_config - Config default value correct: params.max_cpus= 4
nextflow_config - Config default value correct: params.max_memory= 2.GB
nextflow_config - Config default value correct: params.max_time= 1.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
template_strings - Did not find any Jinja template strings (114 files)
schema_lint - Schema 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - LOCIDEX_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - MAP_TO_TSV found in conf/modules.config and Nextflow scripts.
modules_config - ARBORATOR found in conf/modules.config and Nextflow scripts.
modules_config - ARBOR_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - IRIDA_NEXT_OUTPUT found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

nf-core/tools version 2.14.1
Run at 2024-05-29 15:43:10

mattheww95 · 2024-04-10T15:28:32Z

This is an initial commit for for the cluster splitting pipeline, more work will need to be dont to deal with the actual goal the pipeline is supposed to address.

Currently there appears to be some issues in how some files are being constructed e.g. column order changes. This may be due to how the config file specific to arborator is set up.

But this commit can serve as a good starting point for the rest of the pipeline.

apetkau

Thanks so much @mattheww95. Sorry about the long wait for this PR. I just have 2 comments.

apetkau · 2024-05-21T17:18:01Z

.nf-core.yml

@@ -15,9 +15,12 @@ lint:
    - .github/ISSUE_TEMPLATE/bug_report.yml
    - .github/PULL_REQUEST_TEMPLATE.md
    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml


Could the linting_comment.yml and linting.yml files not be added to the files to ignore linting and instead the files themselves updated to match what's found e.g., in here: https://github.com/phac-nml/snvphylnfc/tree/dev/.github/workflows

Thank you for the example! I will take care of that.

Tests are passing locally, but no in actions. Do you have any suggestions on what could resolve the issue? @apetkau

workflows/cluster_splitter.nf

update schema

d5df73d

mattheww95 added 17 commits April 9, 2024 15:10

update black linting

4119f4e

update prettierignore

0bc7bd4

update prettierignore

d943b80

remove module tests

3abb095

updated config paths

e13b702

updated arborview inline shebang to python3

767a1cb

updated arborview permissions

451ab53

updated test profile data

14ef4e4

removed dead code

e6c5ef2

updated test paths

da5b668

updated editroconfig

a8fec1a

updated tests

7173d5d

updated tests

02acb61

updated arborator tests in

6b5fbd1

updated tests output and cases

79f062d

updated permisions on inline arborview script

c690f87

updated files to unchanged ignore

0c8bb72

mattheww95 marked this pull request as ready for review April 10, 2024 15:28

mattheww95 requested a review from apetkau April 10, 2024 15:28

apetkau requested changes May 21, 2024

View reviewed changes

mattheww95 and others added 6 commits May 22, 2024 15:36

Update .nf-core.yml

17bd09b

Update cluster_splitter.nf

7b234b1

Update linting_comment.yml

e244760

Update linting.yml

d6c925e

Update .nf-core.yml

829b019

CI debugging

bfde9bf

emarinier added 8 commits May 23, 2024 10:20

CI debugging

7242743

CI debugging

9dba48f

CI debugging

f6e3561

CI debugging

0f5110a

CI debugging

3f2a824

CI debugging

7cf26d3

CI debugging

347eba5

Attempting to fix CI issues, clean code.

f83d634

emarinier merged commit 3451e15 into dev May 29, 2024
4 checks passed

emarinier deleted the tests/update branch May 29, 2024 16:48

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Initial PR getting tests to pass #1

Initial PR getting tests to pass #1

mattheww95 commented Apr 9, 2024

github-actions bot commented Apr 9, 2024

github-actions bot commented Apr 9, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mattheww95 commented Apr 10, 2024

apetkau left a comment

apetkau May 21, 2024

mattheww95 May 22, 2024

mattheww95 May 22, 2024 •

edited

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Initial PR getting tests to pass #1

Initial PR getting tests to pass #1

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mattheww95 commented Apr 9, 2024

github-actions bot commented Apr 9, 2024

Python linting (black) is failing

github-actions bot commented Apr 9, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mattheww95 commented Apr 10, 2024

apetkau left a comment

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apetkau May 21, 2024

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mattheww95 May 22, 2024

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mattheww95 May 22, 2024 • edited Loading

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Python linting (`black`) is failing

github-actions bot commented Apr 9, 2024 •

edited

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

mattheww95 May 22, 2024 •

edited

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