Patch release V1.1.1 #388

LilyAnderssonLee · 2023-10-03T12:06:17Z

This patch release updated/fixed three aspects:

Update to nf-core pipeline template v2.10
Update the module of KrakenUniq
Add support for previously missing Bracken-corrected Kraken2 report as output

PR checklist

bump version to v1.2.0dev

Correct the tag description and links

Correct git user name

solve the conflicts caused by multiQC version

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

Correct Wrong links in "assets/multiqc_config.yml.

update krakenuniq module

Bracken output report addition

github-actions · 2023-10-03T12:08:32Z

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

Posted for pipeline commit 1099e04

+| ✅ 158 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.1
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
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 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-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: 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: 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: lib/WorkflowTaxprofiler.groovy
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: .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 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-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 - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy 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 (205 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: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcments.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' 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 2.10
Run at 2023-10-10 15:07:04

update the patch release date

Co-authored-by: James A. Fellows Yates <[email protected]>

Update taxpasta module

Co-authored-by: Moritz E. Beber <[email protected]>

Add taxpasta taxdir check

jfy133 · 2023-10-08T13:42:42Z

@nf-core-bot fix linting

maxibor · 2023-10-10T13:11:02Z

Hey @LilyAnderssonLee ,
Any reason to not have #397 here ?
You can just update the changelog in this PR :)

taxpasta dependency update

LilyAnderssonLee · 2023-10-10T17:14:25Z

@maxibor Sorry for a misleading title of that PR. I just added the taxpasta version change information to the CHANGELOG.md which I had forgotten to update in PR #392

LilyAnderssonLee and others added 30 commits September 19, 2023 09:58

bump version to v1.2.0dev

2878c46

Merge branch 'dev' into bump_versions

f4092c6

Merge pull request #376 from LilyAnderssonLee/bump_versions

2e7479b

bump version to v1.2.0dev

Correct tag descriptions

712fdaa

Merge pull request #377 from LilyAnderssonLee/changelog

7800174

Correct the tag description and links

Correct git user name

4b88362

Merge pull request #378 from LilyAnderssonLee/changelog

ba3ec99

Correct git user name

added corrected kraken2 report as output from bracken

ee58c4d

corrected bracken report output definition

c15d035

added line for changes to output

6a5719c

Merge branch 'dev' into bracken_output_report_fix

5f9bfdb

Template update for nf-core/tools version 2.10

5300caf

Merge branch 'dev' into nf-core-template-merge-2.10

388d3cd

Update modules.json

257ccfb

solve the conflicts caused by multiQC version

update krakenuniq module to the latest

e323808

Add PR info

d0f5d72

Update WorkflowTaxprofiler.groovy

43ef576

Update main.nf

53d29f0

bump the version and add the template update PR

1a37d99

bump the version

4176e5b

bump the version

8bac57d

Merge pull request #380 from nf-core/nf-core-template-merge-2.10

aecc88b

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

Update CHANGELOG.md

e86898e

Merge branch 'dev' into krakenuniq

57794ee

add dependencies

6c93ef0

correct PR info

eed5dca

Update CHANGELOG.md

db62778

Update multiqc_config.yml

87ef35a

Correct Wrong links in "assets/multiqc_config.yml.

Merge pull request #383 from LilyAnderssonLee/krakenuniq

84752d0

update krakenuniq module

updated bracken module

2f2224e

jfy133 added 5 commits October 1, 2023 17:33

Merge branch 'dev' into bracken_output_report_fix

0033280

Update conf/modules.config

a29fa7d

Update output.md

1dd9144

Apply suggestions from code review

e6c2cf9

Merge pull request #379 from hkaspersen/bracken_output_report_fix

bd56d37

Bracken output report addition

LilyAnderssonLee requested a review from sofstam October 3, 2023 12:08

LilyAnderssonLee requested a review from jfy133 October 3, 2023 12:08

LilyAnderssonLee and others added 2 commits October 3, 2023 14:18

update the patch release date

1adfee8

Merge pull request #389 from LilyAnderssonLee/patchRelease

671fdf9

update the patch release date

jfy133 approved these changes Oct 3, 2023

View reviewed changes

sofstam approved these changes Oct 4, 2023

View reviewed changes

LilyAnderssonLee and others added 10 commits October 6, 2023 12:01

Update taxpasta module

501baf8

[automated] Fix linting with Prettier

b453a8f

Update CHANGELOG.md

5b0a270

Co-authored-by: James A. Fellows Yates <[email protected]>

[automated] Fix linting with Prettier

503db1a

Add check for taxpasta_add_ and taxonomy

2cbd0c7

Update CHANGELOG.md

ca86c48

Merge pull request #392 from nf-core/taxpasta_v0.6.1

190b2f2

Update taxpasta module

Update CHANGELOG.md

091c065

Update workflows/taxprofiler.nf

0b54be1

Co-authored-by: Moritz E. Beber <[email protected]>

Merge pull request #393 from nf-core/add-taxpasta-taxdir-check

4c2014e

Add taxpasta taxdir check

nf-core-bot and others added 2 commits October 8, 2023 13:43

[automated] Fix linting with Prettier

66fc35e

taxpasta dependency update

cb3f912

LilyAnderssonLee added 2 commits October 10, 2023 15:51

taxpasta dependency update

8a513be

Merge pull request #397 from LilyAnderssonLee/dependency

1099e04

taxpasta dependency update

LilyAnderssonLee merged commit 4add6c9 into master Oct 11, 2023
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Patch release V1.1.1 #388

Patch release V1.1.1 #388

LilyAnderssonLee commented Oct 3, 2023

github-actions bot commented Oct 3, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

jfy133 commented Oct 8, 2023

maxibor commented Oct 10, 2023

LilyAnderssonLee commented Oct 10, 2023

Patch release V1.1.1 #388

Patch release V1.1.1 #388

Conversation

LilyAnderssonLee commented Oct 3, 2023

PR checklist

github-actions bot commented Oct 3, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

jfy133 commented Oct 8, 2023

maxibor commented Oct 10, 2023

LilyAnderssonLee commented Oct 10, 2023

github-actions bot commented Oct 3, 2023 •

edited

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