Important! Template update for nf-core/tools v2.13 #450

nf-core-bot · 2024-02-20T16:07:19Z

Version 2.13 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.13 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.13 release page.

github-actions · 2024-02-22T10:09:49Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 747fe60

+| ✅ 189 tests passed       |+
!| ❗   3 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ 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-taxprofiler_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-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_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 found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-taxprofiler_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowTaxprofiler.groovy
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: 1.1.6dev
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.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.kmcp_mode= 3
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
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.igenomes_base= s3://ngi-igenomes/igenomes/
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/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/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-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_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
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (268 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: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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' 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'

Run details

nf-core/tools version 2.13.1
Run at 2024-02-29 18:14:04

Template update for nf-core/tools version 2.13

1041602

sofstam force-pushed the nf-core-template-merge-2.13 branch 2 times, most recently from e29d7e0 to 1041602 Compare February 22, 2024 16:30

LilyAnderssonLee and others added 16 commits February 26, 2024 14:25

Merge template 2.13

446bf91

Remove merger

d2e49b0

Remove merger

616fbea

Fix conflict

7111412

fix the conflicts between branches

1cd0011

fix the conflicts

f2a69e4

add doi

fe2661c

Update the module falco and fix the merge marker

6a2ce11

add groovy.text to SimpleTemplateEngine

3cebac5

remove groovy codes

4278694

remove groovy codes

64652c6

add database channel to main.nf

338f6fa

remove redundant definition of FASTQC & MULTIQC

35171b1

add definition of adapterlist

e913c8a

fix methodsDescriptionText in utils_nfcore_taxprofiler_pipeline

f31a8e8

check the motus_db in ci.yml

41c26b6

LilyAnderssonLee force-pushed the nf-core-template-merge-2.13 branch from 023e4b2 to 41c26b6 Compare February 29, 2024 10:43

add absolute path of db_mOTU in ci.yml

747fe60

nf-core-bot closed this Mar 1, 2024

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Important! Template update for nf-core/tools v2.13 #450

Important! Template update for nf-core/tools v2.13 #450

nf-core-bot commented Feb 20, 2024

github-actions bot commented Feb 22, 2024 •

edited

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❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Important! Template update for nf-core/tools v2.13 #450

Important! Template update for nf-core/tools v2.13 #450

Conversation

nf-core-bot commented Feb 20, 2024

github-actions bot commented Feb 22, 2024 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

github-actions bot commented Feb 22, 2024 •

edited

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`nf-core lint` overall result: Failed ❌