Patch release 1.1.1 #276

jasmezz · 2023-05-17T14:41:03Z

v1.1.1 - [2023-05-17]

`Added`

#270 Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
#274 Update all modules: changed docker links according to the change of quay.io as default repository. (by @jasmezz)
#275 Save DRAMP database in the common database directory if --save_databases is supplied. (by @jasmezz)

`Fixed`

#272 Fix typo in Prokka output path in modules.config. (by @jasmezz)
#237 Update Ampir module after input bugfix in module. (reported by @mathavanpu, fix by @louperelo)

`Dependencies`

`Deprecated`

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
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).

Post-release version bump

Because not all modules use quay as container repo (like gunzip, tar), those have to be updated before the new feature works.

Important! Template update for nf-core/tools v2.8

Fix prokka in `modules.config`

Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>

Update ampir module

Save DRAMP in common database dir

Update (almost) all modules

github-actions · 2023-05-17T15:32:33Z

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

Posted for pipeline commit 80564c6

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.1.1'
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered 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-funcscan_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-funcscan_logo_light.png
files_exist - File found: docs/images/nf-core-funcscan_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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowFuncscan.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: .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-funcscan_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.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.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-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_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
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: 22.10.1, Config: 22.10.1
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 (157 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: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.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
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 2.8
Run at 2023-05-24 13:58:31

tower.yml

modules/nf-core/pyrodigal/main.nf

tower.yml

CHANGELOG.md

ramprasadn

LGTM! 🚀

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

jasmezz and others added 30 commits April 28, 2023 00:09

Version bump + correct last release date

33a438c

Correct version

ea4820a

Template update for nf-core/tools version 2.8

91eb532

Merge pull request #269 from nf-core/post-release-version-bump

2c84798

Post-release version bump

Merge branch 'dev' into nf-core-template-merge-2.8

df9a4c8

Fix error in resolving merge conflict

9b0989e

Switch quay default off (temporarily), fix typo

03f86fa

Because not all modules use quay as container repo (like gunzip, tar), those have to be updated before the new feature works.

Fix linting (update modules)

46fd731

Update modules (for new quay feature to work)

4abee09

Update CHANGELOG.md [skip ci]

735a566

Merge pull request #270 from nf-core/nf-core-template-merge-2.8

d79057b

Important! Template update for nf-core/tools v2.8

Fix prokka path

9357d92

Update changelog

49d89f7

Fix linting

7179823

Fix linting

cd9c3ed

Merge pull request #272 from nf-core/fix-modules-config

9570218

Fix prokka in `modules.config`

update ampir module

5d684b5

update changelog

d76d924

Apply suggestions from code review

36779d8

Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>

Merge pull request #273 from louperelo/updateamplify

21a71e7

Update ampir module

Pull all module updates + update local module

a40a086

Update changelog

02edf73

Save DRAMP download in common database dir

1af35bd

Update pyrodigal + respective AMP subworkflow

efa9b5a

Update combgc.nf

c9b2bc6

Add DRAMP directory in docs [skip ci]

4f901c5

Merge pull request #275 from nf-core/dramp-directory

d0a1633

Save DRAMP in common database dir

Merge branch 'dev' into update-modules

930b091

Merge pull request #274 from nf-core/update-modules

c28ffa5

Update (almost) all modules

Release version bump

a8000c5

ramprasadn reviewed May 19, 2023

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jfy133 reviewed May 24, 2023

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jasmezz added 2 commits May 24, 2023 15:36

Fix pyrodigal entry in modules.config

6aa0605

Update changelog

80564c6

jasmezz requested review from jfy133 and ramprasadn May 24, 2023 15:04

jfy133 approved these changes May 24, 2023

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ramprasadn approved these changes May 24, 2023

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Apply suggestions from code review [skip ci]

304ff84

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

jasmezz merged commit 34063c4 into master May 24, 2023
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Patch release 1.1.1 #276

Patch release 1.1.1 #276

jasmezz commented May 17, 2023

github-actions bot commented May 17, 2023 •

edited

❗ Test warnings:

✅ Tests passed:

Run details

ramprasadn left a comment

Patch release 1.1.1 #276

Patch release 1.1.1 #276

Conversation

jasmezz commented May 17, 2023

v1.1.1 - [2023-05-17]

Added

Fixed

Dependencies

Deprecated

PR checklist

github-actions bot commented May 17, 2023 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

ramprasadn left a comment

Choose a reason for hiding this comment

`Added`

`Fixed`

`Dependencies`

`Deprecated`

github-actions bot commented May 17, 2023 •

edited

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