Dev -> Master 2.5.0 #347

edmundmiller · 2023-10-18T08:32:23Z

No description provided.

bump version 2.5.0dev

Adding publish mode for coverage2cytosine NOMe-seq filtered GpC coverage files.

Added comment for coverage2cytosine publishing of files.

Some other module updates are available, but those will require changes to the pipeline code.

Publish coverage files

Important! Template update for nf-core/tools v2.9

Apply easy module updates

Updated zymo preset "--clip_r2" argument value from 15 to 10.

Updated all em_seq preset argument values from 8 to 10.

Wrong display values for "zymo" and "em_seq" presets on help page

Use fromSamplesheet

support pipeline-specific configs

Support pipeline-specific configs

Maintainers

…-2.10

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

And the fasta index regex

Add exists to Schema

Citationtools

github-actions · 2023-10-18T08:35:09Z

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

Posted for pipeline commit e02fd8c

+| ✅ 153 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.5.0

❔ Tests ignored:

files_exist - File is ignored: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: .gitattributes
actions_ci - actions_ci
multiqc_config - multiqc_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: .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-methylseq_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-methylseq_logo_light.png
files_exist - File found: docs/images/nf-core-methylseq_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/WorkflowMethylseq.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-methylseq_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 - .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-methylseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-methylseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-methylseq_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_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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (133 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: 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: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting.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 2.10
Run at 2023-10-18 10:03:07

I refuse to update this every release. Co-authored-by: sateeshperi <[email protected]>

Release Prep for 2.5.0

FelixKrueger

LGTS. Very nice work!

sateeshperi

LGTF&S

let's go

sateeshperi and others added 30 commits June 12, 2023 14:33

bump version 2.5.0dev

86d73c7

Merge pull request #326 from sateeshperi/dev

13cb0fe

bump version 2.5.0dev

Template update for nf-core/tools version 2.9

5ece807

Update modules.config

9e2d80f

Adding publish mode for coverage2cytosine NOMe-seq filtered GpC coverage files.

Update CHANGELOG.md

107f736

Added comment for coverage2cytosine publishing of files.

Apply easy module updates

e048710

Some other module updates are available, but those will require changes to the pipeline code.

Changelog

ace1a39

Merge pull request #331 from FelixKrueger/publish_coverage_files

e576ec8

Publish coverage files

Merge branch 'dev' into nf-core-template-merge-2.9

6afd472

Merge pull request #329 from nf-core/nf-core-template-merge-2.9

b565c21

Important! Template update for nf-core/tools v2.9

Merge branch 'dev' into master

b58eb2a

Merge pull request #333 from ewels/master

76ef5de

Apply easy module updates

Update nextflow_schema.json

2caf09e

Updated zymo preset "--clip_r2" argument value from 15 to 10.

Update nextflow_schema.json

591cc41

Updated all em_seq preset argument values from 8 to 10.

Merge pull request #335 from update_kit_schema

16007cf

Wrong display values for "zymo" and "em_seq" presets on help page

refactor: Use fromSamplesheet instead of input_check

7910cc1

fix: Add some magic from rnaseq

47d631c

chore: Update CHANGELOG

b6bb69f

chore: Update snapshots

675f73c

update tests, snapshots and ci

0cd09ec

Merge pull request #341 from nf-core/fromSamplesheet

89b0aa4

Use fromSamplesheet

Update nextflow.config

1737eda

support pipeline-specific configs

Merge pull request #343 from nf-core/maxulysse-patch-1

c5bbf8e

Support pipeline-specific configs

Template update for nf-core/tools version 2.10

8e2a6f3

docs: Update Maintainers

ee70918

chore: Add CODEOWNERS file

766a26b

chore: Update CHANGELOG

92312de

Merge pull request #345 from nf-core/maintainers

0fe9fbd

Maintainers

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

4ae729b

…-2.10

Merge pull request #344 from nf-core/nf-core-template-merge-2.10

8e1411a

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

edmundmiller and others added 13 commits October 16, 2023 19:01

feat: Add exists to schema

aa24e65

feat: Add patterns to schema

f795c9a

fix(schema): Update formats and exists

93cd17c

And the fasta index regex

chore: Update CHANGELOG

3d63bca

Merge pull request #342 from nf-core/schema-exists

b5727f7

Add exists to Schema

chore: Remove a TODO that was done

4a747e0

chore(#336): Add most of tools to citations bibtex

e457cde

chore(#336): Add tools citations

d1adc92

feat(#336): Try adding a fancy join

d2d652f

chore(#336): Update reference text

a8bb3b4

chore: Add a note to update TrimGalore Citation

bd1a33f

style: Run bib through citations

157d807

Merge pull request #346 from nf-core/citationtools

d8a759e

Citationtools

edmundmiller added this to the 2.5.0 milestone Oct 18, 2023

edmundmiller self-assigned this Oct 18, 2023

edmundmiller marked this pull request as draft October 18, 2023 08:35

edmundmiller added 2 commits October 18, 2023 10:45

chore: Add issues that were missed and add date

e6db8a8

chore: Bump version

ee11838

edmundmiller requested review from a team and FelixKrueger October 18, 2023 08:54

sateeshperi and others added 4 commits October 18, 2023 09:10

add emojis to changelog v2.5.0

45c4468

bump snapshots for 2.5.0 release

1814838

style: Ignore MultiQC config

f4fe5fd

I refuse to update this every release. Co-authored-by: sateeshperi <[email protected]>

Merge pull request #348 from nf-core/release-prep

e02fd8c

Release Prep for 2.5.0

edmundmiller marked this pull request as ready for review October 18, 2023 09:45

FelixKrueger approved these changes Oct 18, 2023

View reviewed changes

sateeshperi approved these changes Oct 18, 2023

View reviewed changes

edmundmiller merged commit 053e59e into master Oct 18, 2023
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Dev -> Master 2.5.0 #347

Dev -> Master 2.5.0 #347

edmundmiller commented Oct 18, 2023

github-actions bot commented Oct 18, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

FelixKrueger left a comment

sateeshperi left a comment

Dev -> Master 2.5.0 #347

Dev -> Master 2.5.0 #347

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edmundmiller commented Oct 18, 2023

github-actions bot commented Oct 18, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

FelixKrueger left a comment

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github-actions bot commented Oct 18, 2023 •

edited

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