Merging dev into main for Initial Release #6

emarinier · 2025-03-07T17:48:25Z

No description provided.

…ort other transformations.

Adds the Lock Transformation

Adds the Calculate Age Transformation

Updating Regex to Allow Spaces, Disallow Tabs

Fixing Lint Problems

github-actions · 2025-03-07T17:49:40Z

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

Posted for pipeline commit 1c9fcd4

+| ✅ 142 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-metadatatransformation_logo_light.png
files_exist - File is ignored: docs/images/nf-core-metadatatransformation_logo_light.png
files_exist - File is ignored: docs/images/nf-core-metadatatransformation_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/WorkflowMetadatatransformation.groovy
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: ro-crate-metadata.json
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.max_cpus
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: 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-metadatatransformation_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-metadatatransformation_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-metadatatransformation_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/metadatatransformation/metadatatransformation/.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-metadatatransformation_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: 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 - Found nf-validation plugin
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: 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 - Config manifest.version ends in dev: 1.0.0dev
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.transformation= lock
nextflow_config - Config default value correct: params.age_header= age
nextflow_config - Config default value correct: params.metadata_1_header= metadata_1
nextflow_config - Config default value correct: params.metadata_2_header= metadata_2
nextflow_config - Config default value correct: params.metadata_3_header= metadata_3
nextflow_config - Config default value correct: params.metadata_4_header= metadata_4
nextflow_config - Config default value correct: params.metadata_5_header= metadata_5
nextflow_config - Config default value correct: params.metadata_6_header= metadata_6
nextflow_config - Config default value correct: params.metadata_7_header= metadata_7
nextflow_config - Config default value correct: params.metadata_8_header= metadata_8
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 - .github/workflows/linting.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
plugin_includes - No wrong validation plugin imports have been found
template_strings - Did not find any Jinja template strings (0 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: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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 - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - TRANSFORM_METADATA 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: 3.2.0

Run details

nf-core/tools version 3.2.0
Run at 2025-03-07 17:49:21

emarinier added 30 commits January 23, 2025 12:59

Adding locking parameter.

10828a0

Basic CSV writing, IRIDA plugin not working.

6805867

Adding lock module.

e09d346

Channel operator for manually adding IDs to valid IDs.

32f44d0

Adding metadata.

f2fd862

Adding support for sample IDs and Irida IDs.

26e35e1

Updating to match latest plugin code, outputting both IDs.

b8c3112

Linting fixes.

3a182e4

Missing newlines.

0e7860e

Setting up basic tests.

20c1f9c

Parameter tests.

cdf4a54

More tests.

2acfcea

Updating docs.

da16c13

Changing lock/locked.csv to transformation/transformation.csv to supp…

cc134da

…ort other transformations.

Prettier

50aa0cf

Formatting

e0accb3

Correcting ID/sample/sample_name problems.

2de1af1

Moving iridanext config to different file.

a432a04

nf-core lint files changed

a0140a2

Adding ignores.

cbf319e

Setting nf-core version.

2cf979b

Merge pull request #1 from phac-nml/lock

f2d736b

Adds the Lock Transformation

Splitting human and machine-readable outputs.

5315d53

Removing unused file.

c060f19

Switching over to Python-based solution.

be2598d

Adding age transformation.

6e327ee

Removing unused file.

22fdd62

Formatting ages better.

772c9c7

Error handling.

649bc2d

Handling blank entries.

041e67e

emarinier added 22 commits February 21, 2025 14:33

Ability to specify output age header name.

cfdaed6

Fixes, age_header parameter.

9bc3f09

New test struction, race condition happening.

3e285b5

Fixing race condition bug.

fc7403b

Basic tests set up.

e10d74b

Mixed success and failures test, pandas.NA -> numpy.nan.

0990139

Specifying parameters tests.

03afd35

Remove TODO

e288ccc

Adding missing test data.

47f7497

Updating the documentation.

02db761

Removing trailing whitespace.

e0912a5

Prettier

3d0185e

Adding docker profile.

f99066d

Adding floor to age formatting.

60b5333

Checking key is not added to output.

a6d4635

More details about columns.

d11ab2e

Merge pull request #3 from phac-nml/age

c1b8d91

Adds the Calculate Age Transformation

Updating regex to allow spaces, disallow tabs.

d0cb4d6

Tests, robustness.

674c433

Fixing lint problems.

99c29b7

Merge pull request #4 from phac-nml/update/regex

bcd7a00

Updating Regex to Allow Spaces, Disallow Tabs

Merge pull request #5 from phac-nml/fix/lint

1c9fcd4

Fixing Lint Problems

emarinier self-assigned this Mar 7, 2025

emarinier merged commit 8316af2 into main Mar 7, 2025
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Merging dev into main for Initial Release #6

Merging dev into main for Initial Release #6

emarinier commented Mar 7, 2025

github-actions bot commented Mar 7, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Merging dev into main for Initial Release #6

Merging dev into main for Initial Release #6

Conversation

emarinier commented Mar 7, 2025

github-actions bot commented Mar 7, 2025 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Mar 7, 2025 •

edited

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