Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

svarona · 2024-01-08T11:00:04Z

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2024-01-08T11:01:53Z

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

Posted for pipeline commit 8df9b78

+| ✅ 150 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_exist - File not found: conf/igenomes.config
files_exist - File not found: lib/WorkflowViralrecon.groovy
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
system_exit - System.exit in nanopore.nf: System.exit(1) [line 237]

❔ Tests ignored:

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: lib/NfcoreTemplate.groovy
multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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: 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-viralrecon_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-viralrecon_logo_light.png
files_exist - File found: docs/images/nf-core-viralrecon_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: conf/base.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-viralrecon_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: .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: 2.7.0dev
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
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/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 - .github/workflows/linting.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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
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 (442 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
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.11.1
Run at 2024-01-16 12:40:20

maxulysse · 2024-01-08T15:40:28Z

so this is to replace #407 ?

svarona · 2024-01-08T15:48:08Z

so this is to replace #407 ?

Yes, exactly. I made it in other branch so I won't break anything. I can make it in another branch if you prefer.

maxulysse · 2024-01-09T11:00:49Z

so this is to replace #407 ?

Yes, exactly. I made it in other branch so I won't break anything. I can make it in another branch if you prefer.

no worries about that, thanks a lot

maxulysse · 2024-01-11T14:01:04Z

I put this PR as ready for review

svarona · 2024-01-11T14:24:40Z

I put this PR as ready for review

Ok, thank you! We keep working on the medaka model error

maxulysse · 2024-01-11T14:49:02Z

I put this PR as ready for review

Ok, thank you! We keep working on the medaka model error

I'll try to review ASAP

main.nf

nextflow.config

nf-core-bot and others added 30 commits September 26, 2023 08:08

Template update for nf-core/tools version 2.10

0b1e295

Merge branch 'TEMPLATE' into dev_template

ce82ef6

Fixed notes

977d069

Fixed a header

a90a257

Fixed biocontainers

4976471

Added missing change

66be601

Fixed quay.io

67f531e

removed quay.io from main.nf

0fd940b

Fixed again quay.io

b6804f5

Fixed test2

9da284a

Fixed module

c3a677d

mas test

ff372f7

removed duplicated line

a507d99

Template update for nf-core/tools version 2.11

9e0a1c2

updated modules

20dc34d

fixing modules call according to updates

7f2923b

Fixed lint

3bd897e

Template update for nf-core/tools version 2.11.1

48f8032

Merge branch 'TEMPLATE' into dev_template

55bfa3a

Merge branch 'TEMPLATE' into dev_template

3c7778c

Fix prettier

fa532f6

pixed prettier

dcc56b2

Fixed some conflicts

bf5fd9d

Updated modules

28ce0d2

Fixed quast process

a8ce52a

Fixed quast for multiqc

8d57896

Fixed ref fasta channel

5d63daf

Fixed ref fasta channel

96cdeb7

Fixed empty channels

cfea905

Fixed mosdepth process

eb7a82d

svarona added 8 commits December 27, 2023 15:23

Fixed empty fields

6d5b405

Fixed quast

ad5b38a

Fixed mosdepth

5ccac08

Fixed empty channels

78a4143

Fixed fasta channel

661ec68

Fixed gff channel for empty path

508e270

Fixed prettier

566837a

Fixed empty channels

bb66560

svarona changed the title ~~Fixed conflicts and updated modulels for nf-core/tools version 2.11~~ Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 Jan 8, 2024

maxulysse marked this pull request as ready for review January 11, 2024 14:00

maxulysse mentioned this pull request Jan 11, 2024

Important! Template update for nf-core/tools v2.11.1 #407

Closed

Download medaka model for nanopore test

b3d2dbb

adamrtalbot approved these changes Jan 16, 2024

View reviewed changes

maxulysse reviewed Jan 16, 2024

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maxulysse reviewed Jan 16, 2024

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svarona added 2 commits January 16, 2024 13:08

Removed TODO comment

249146a

Removed igenomes_base

4c850ba

maxulysse reviewed Jan 16, 2024

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removed igenomes_base from validationSchemaIgnoreParams

8df9b78

maxulysse approved these changes Jan 16, 2024

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svarona merged commit be0473b into nf-core:dev Jan 16, 2024
24 checks passed

svarona deleted the dev_template branch January 17, 2024 15:52

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Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

svarona commented Jan 8, 2024

github-actions bot commented Jan 8, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Jan 8, 2024

svarona commented Jan 8, 2024 •

edited

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maxulysse commented Jan 9, 2024

maxulysse commented Jan 11, 2024

svarona commented Jan 11, 2024

maxulysse commented Jan 11, 2024

Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

Conversation

svarona commented Jan 8, 2024

PR checklist

github-actions bot commented Jan 8, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Jan 8, 2024

svarona commented Jan 8, 2024 • edited Loading

maxulysse commented Jan 9, 2024

maxulysse commented Jan 11, 2024

svarona commented Jan 11, 2024

maxulysse commented Jan 11, 2024

github-actions bot commented Jan 8, 2024 •

edited

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

svarona commented Jan 8, 2024 •

edited

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