Update Modules #147

edmundmiller · 2024-07-20T16:09:43Z

No description provided.

github-actions · 2024-07-20T16:12:02Z

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

Posted for pipeline commit 0319bc1

+| ✅ 196 tests passed       |+
#| ❔   4 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 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 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!

❔ Tests ignored:

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/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
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-nascent_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-nascent_logo_light.png
files_exist - File found: docs/images/nf-core-nascent_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-nascent_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/WorkflowNascent.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: 2.3.0dev
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.aligner= bwa
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.human_pangenomics_base= https://s3-us-west-2.amazonaws.com/human-pangenomics
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.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.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 - .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 - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-nascent_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nascent_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nascent_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 (452 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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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 - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - DRAGMAP_HASHTABLE found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_CCURVE found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_GENOMECOV_PLUS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_GENOMECOV_MINUS found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_BAMCOVERAGE_PLUS found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_BAMCOVERAGE_MINUS found in conf/modules.config and Nextflow scripts.
modules_config - DREG_PREP found in conf/modules.config and Nextflow scripts.
modules_config - SUBREAD_FEATURECOUNTS_GENE found in conf/modules.config and Nextflow scripts.
modules_config - SUBREAD_FEATURECOUNTS_PREDICTED found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDPEAKS found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_MAKETAGDIRECTORY found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_MAKEUCSCFILE found in conf/modules.config and Nextflow scripts.
modules_config - PINTS_CALLER found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT 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 2024-07-22 21:36:32

https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci

#148

edmundmiller · 2024-07-22T21:46:40Z

Merging, IDK what's going on with #148

edmundmiller self-assigned this Jul 20, 2024

edmundmiller added 5 commits July 20, 2024 11:26

style: Try to fix linting

25d8803

build: Remove extra "groseq" workflow

0280009

chore: nf-core modules update

47ba2f4

fix: Catch up with module updates

64acae7

chore: nf-core modules update subworkflow

ed8510f

edmundmiller force-pushed the update-modules branch from 59e3d0f to ed8510f Compare July 20, 2024 23:02

ci: Bump detect-nf-test-changes to 0.0.3

45455b6

maxulysse approved these changes Jul 22, 2024

View reviewed changes

edmundmiller added 5 commits July 22, 2024 14:11

style: Fix CI triggers

f41ddfd

https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci

style: Minimum pipeline NF version

9226907

https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci

style: Ignore ci.yml

1582d2b

chore: nf-core subworkflows update

f5ae7ff

style: Remove stray comment update

2801dea

edmundmiller force-pushed the update-modules branch from 99165f5 to 2801dea Compare July 22, 2024 19:11

edmundmiller added 2 commits July 22, 2024 16:06

test: Update snapshot for GitHub actions

cc8cc7e

test: Skip preseq in BWA test

0319bc1

#148

edmundmiller force-pushed the update-modules branch from f234dbf to 0319bc1 Compare July 22, 2024 21:34

edmundmiller marked this pull request as ready for review July 22, 2024 21:46

edmundmiller added this to the 2.3.0 milestone Jul 22, 2024

edmundmiller merged commit 9954adf into dev Jul 22, 2024
12 checks passed

edmundmiller deleted the update-modules branch July 22, 2024 21:46

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Update Modules #147

Update Modules #147

edmundmiller commented Jul 20, 2024

github-actions bot commented Jul 20, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Jul 22, 2024

Update Modules #147

Update Modules #147

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edmundmiller commented Jul 20, 2024

github-actions bot commented Jul 20, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

edmundmiller commented Jul 22, 2024

github-actions bot commented Jul 20, 2024 •

edited

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