Template update from 2.3 to 2.3.2 #11

ypriverol · 2022-03-24T14:03:15Z

PR checklist

u

minor fix

…core/quantms into dev � Conflicts: � .github/workflows/awsfulltest.yml � .github/workflows/awstest.yml � .github/workflows/ci.yml � .yamllint.yml � CHANGELOG.md � CITATIONS.md � README.md � assets/multiqc_config.yaml � docs/output.md � docs/usage.md � modules.json � modules/nf-core/modules/fastqc/main.nf � modules/nf-core/modules/fastqc/meta.yml � nextflow.config � nextflow_schema.json

Co-authored-by: Julianus Pfeuffer <[email protected]>

Template updated 2.3.1

github-actions · 2022-03-24T14:04:14Z

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

Posted for pipeline commit 6f2f79b

+| ✅ 145 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0'

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config

✅ 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: .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-quantms_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-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_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/NfcoreSchema.groovy
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: assets/multiqc_config.yml
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: lib/WorkflowQuantms.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
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-quantms_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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.version
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 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 .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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
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/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-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_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 - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore 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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (151 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.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
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'.

Run details

nf-core/tools version 2.3.2
Run at 2022-03-24 14:03:57

Template update 2.3.2

� Conflicts: � modules/local/openms/thirdparty/luciphoradapter/meta.yml � modules/local/sdrfparsing/meta.yml

� Conflicts: � modules/local/openms/thirdparty/luciphoradapter/meta.yml

updates

u

Template update for nf-core/tools version 2.11

daichengxin and others added 30 commits March 22, 2022 22:30

Merge pull request #13 from bigbio/dev

56b4a88

u

update

d2a3798

fixed

84f4b1e

FIXED

864b7ee

Merge pull request #135 from daichengxin/dev

ddfb928

minor fix

Template update for nf-core/tools version 2.3.1

72b33a1

minor changes

135fdaf

minor changes

e7b4ebe

minor changes

72f1c19

minor changes

d38d4c1

minor changes

fb74298

minor changes

6f10750

minor changes

2e3d456

minor changes

bbc52cc

prettier changes

93459b6

prettier changes

1def9ba

prettier changes

f11a319

Update docs/usage.md

87233f5

Co-authored-by: Julianus Pfeuffer <[email protected]>

minor changes

72677e9

minor changes

572afcc

multiqc updated

d2cbdfb

multiqc updated

5da3760

fix

29e2066

fix

194b185

fix?

ebfd932

fix

d05b215

fix prettier?

2eec482

revert the space changes

ef8a70e

remove unnecessary lint exceptions?

aa21791

jpfeuffer added 2 commits March 24, 2022 14:56

Merge pull request #139 from ypriverol/dev

6f2f79b

Template updated 2.3.1

Template update 2.3.2

398288b

Merge pull request #142 from bigbio/template-update-2-3-2

ae3eeab

Template update 2.3.2

jpfeuffer changed the title ~~Template 2.3.1 updated~~ Template update from 2.3 to 2.3.2 Mar 24, 2022

jpfeuffer mentioned this pull request Mar 24, 2022

Important! Template update for nf-core/tools v2.3.2 #10

Closed

jpfeuffer approved these changes Mar 24, 2022

View reviewed changes

ypriverol and others added 9 commits March 24, 2022 14:53

Merge branch 'dev' into dev

c86f556

Merge branch 'dev' of https://github.com/nf-core/quantms into dev

203f8bf

� Conflicts: � modules/local/openms/thirdparty/luciphoradapter/meta.yml � modules/local/sdrfparsing/meta.yml

multiqc updated

f828b66

Merge remote-tracking branch 'origin/dev' into dev

4f16d50

Merge branch 'dev' of https://github.com/bigbio/quantms into dev

df78288

� Conflicts: � modules/local/openms/thirdparty/luciphoradapter/meta.yml

multiqc updated

dcae64d

multiqc updated

a939826

multiqc updated

55b92bc

Merge pull request #143 from ypriverol/dev

2935cb5

updates

jpfeuffer closed this Mar 24, 2022

jpfeuffer reopened this Mar 24, 2022

jpfeuffer merged commit 66fe560 into nf-core:dev Mar 24, 2022

jpfeuffer pushed a commit that referenced this pull request Apr 21, 2022

Merge pull request #11 from bigbio/dev

213aebb

u

jpfeuffer pushed a commit that referenced this pull request Aug 12, 2022

Merge pull request #11 from bigbio/dev

6c52a21

u

jspaezp referenced this pull request in TalusBio/quantms Jan 9, 2024

Merge pull request bigbio#11 from daichengxin/nf-template

788bd79

Template update for nf-core/tools version 2.11

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Template update from 2.3 to 2.3.2 #11

Template update from 2.3 to 2.3.2 #11

ypriverol commented Mar 24, 2022

github-actions bot commented Mar 24, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Template update from 2.3 to 2.3.2 #11

Template update from 2.3 to 2.3.2 #11

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ypriverol commented Mar 24, 2022

PR checklist

github-actions bot commented Mar 24, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Mar 24, 2022 •

edited

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