Release 1.5.4 #297

nschcolnicov · 2024-12-04T12:26:19Z

1.5.4 - 2024-12-03

`Added`

`Changed`

#291 Updated samshee module to the latest version
#296 Bump to version 1.5.4.

`Fixed`

#288 Fix test_full by validating parameters in lenientMode and fix workflow megatest workflow dispatch.
#294 Fix workflow.onComplete email sending feature.

Post 1.5.3 release version bump

…is true

This reverts commit 68776c6.

…in samshee

Fix parameter validation in `test_full` and workflow dispatch

Bump samshee

Fixed email

Bump versions for 1.5.4 release

github-actions · 2024-12-04T12:28:16Z

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

Posted for pipeline commit e09e79b

+| ✅ 206 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 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

❔ 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: conf/igenomes_ignored.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 - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 does not contain dev for release: 1.5.4
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.demultiplexer= bclconvert
nextflow_config - Config default value correct: params.strandedness= auto
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.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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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 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 - 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.
modules_config - SAMSHEE found in conf/modules.config and Nextflow scripts.
modules_config - FASTQ_TO_SAMPLESHEET 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: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-06 14:31:01

…fix_merge_issues

Merging changes from master into dev to 1.5.4 fix release merging issues

atrigila · 2024-12-06T13:08:28Z

.nf-core.yml

  skip_features:
    - igenomes
-  version: 1.5.2
+  version: 1.5.3dev


shouldn't it be 1.5.4 here?

You are right 🤦

bump version in .nf-core.tml

atrigila and others added 21 commits November 6, 2024 15:39

post patch version bump

eccff31

Merge pull request #287 from atrigila/dev

74059b2

Post 1.5.3 release version bump

test: fix workflow dispatch

e4f429e

test: add lenient mode to fix parameter validation in test full

3a69cc5

test: enforce meta.id always be a string after nf-schema lenientMode …

09877da

…is true

test: load test profile configs first

68776c6

Revert "test: load test profile configs first"

e8e1815

This reverts commit 68776c6.

tests: update tests

66a07db

test: add modules config afterwards to solve pass ext.args correctly …

46fc312

…in samshee

test: include samshee config only for correct v1_schema

28cd3db

Merge pull request #290 from atrigila/check_test_full

7bce648

Fix parameter validation in `test_full` and workflow dispatch

Bump samshee

751badd

Added latest version of samshee

cdb42c5

Merge pull request #291 from nf-core/bump-samshee

d435adb

Bump samshee

Fixed email

47a36c8

Fix changelog PR number

4775973

Updated utils_nfcore_pipeline subworkflow

f6022b5

Merge pull request #294 from nf-core/automation_hook_fix

10b110f

Fixed email

Bump versions for 1.5.4 release

e88837b

Update versions

7fe86df

Merge pull request #296 from nf-core/patch_release

5b96e5e

Bump versions for 1.5.4 release

nschcolnicov requested a review from a team as a code owner December 4, 2024 12:26

nschcolnicov requested review from glichtenstein and removed request for a team December 4, 2024 12:26

nschcolnicov mentioned this pull request Dec 4, 2024

make 1.5.4 patch release of demultiplex #293

Closed

1 task

apeltzer approved these changes Dec 4, 2024

View reviewed changes

nschcolnicov and others added 2 commits December 4, 2024 21:40

Merge branch 'master' of https://github.com/nf-core/demultiplex into …

2702748

…fix_merge_issues

Merge pull request #298 from nf-core/fix_merge_issues

9ea845e

Merging changes from master into dev to 1.5.4 fix release merging issues

nschcolnicov requested a review from atrigila December 6, 2024 12:35

atrigila reviewed Dec 6, 2024

View reviewed changes

atrigila approved these changes Dec 6, 2024

View reviewed changes

nschcolnicov and others added 2 commits December 6, 2024 13:46

bump version in .nf-core.tml

50193d8

Merge pull request #300 from nf-core/bump_missing_versions

e09e79b

bump version in .nf-core.tml

nschcolnicov merged commit ea06178 into master Dec 6, 2024
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Release 1.5.4 #297

Release 1.5.4 #297

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nschcolnicov commented Dec 4, 2024 •

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1.5.4 - 2024-12-03

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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nschcolnicov commented Dec 4, 2024 •

edited

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`Added`

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`Fixed`

github-actions bot commented Dec 4, 2024 •

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