Dev -> Master 2.6.0 #369

edmundmiller · 2024-01-05T18:27:40Z

Double check I didn't miss a version to bump somewhere por favor

post-release dev bump version and snapshots

Replace simple quotes by double quotes for ignore_r1 parameters.

Added a log for the fix

Fix expansion of ignore_r1 parameters in modules.config

https://github.com/nf-core/fetchngs/blob/a7ab1a20bab13b5ba16065071d593192592e3411/nf-test.config

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

Again Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

Co-authored-by: sateeshperi <sateeshperi@users.noreply.github.com>

Add scatter CI

Duplicates behavior from #360

Co-authored-by: FelixKrueger <FelixKrueger@users.noreply.github.com>

No groups

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

github-actions · 2024-01-05T18:29:17Z

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

Posted for pipeline commit 0bc1575

+| ✅ 154 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.6.0

❔ 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
nextflow_config - nextflow.config contains configuration profile test
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 (149 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: 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 2024-01-05 20:42:55

sateeshperi · 2024-01-05T18:54:28Z

need to bump version in snapshots

FelixKrueger

LGTM, go for it!

sateeshperi and others added 30 commits October 29, 2023 10:35

post-release dev bump version and snapshots

d65d8aa

Merge pull request #356 from sateeshperi/dev

fb8ff2e

post-release dev bump version and snapshots

fix for bug #354 - dev branch

6cb25ee

Update modules.config

03880b0

Replace simple quotes by double quotes for ignore_r1 parameters.

Update CHANGELOG.md

3c6f816

Added a log for the fix

chore: Update CHANGELOG

bc60097

Merge branch 'dev' into master

f981cbf

Merge pull request #359 from noecochetel/master

7ec570c

Fix expansion of ignore_r1 parameters in modules.config

ci: Add scatter CI

57f3e4c

ci: Bump nf-test

7aca73b

test: Mark bwameth index generation as failing

23c48d5

test: Mark all index tests as failing

7d2146c

build: nf-core modules install untar

31b23b7

feat: Add untar for indexs

fa6ffc4

test: Remove tests depending on other tests

0a7bcac

test: Copy nf-test config from fetchngs

98c4f8b

https://github.com/nf-core/fetchngs/blob/a7ab1a20bab13b5ba16065071d593192592e3411/nf-test.config

ci: Don't upload test report

0c46466

Template update for nf-core/tools version 2.11

5f8e463

Template update for nf-core/tools version 2.11.1

db62e2a

Make index file check more precise

8966c13

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

Fix test indexes

438ceff

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

test: Update test lib path

2673007

ci: Bump nf-test version

ab3898b

Again Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

test: Bump snapshots for nf-test 0.8.2

9d88d67

Co-authored-by: sateeshperi <sateeshperi@users.noreply.github.com>

Merge pull request #350 from nf-core/scatter

d6b50b7

Add scatter CI

test: Move test samplesheet to assets

7155cc6

test: Remove _'s in one sample

cc1b937

Duplicates behavior from #360

fix(#360): Return id when sample field has no _'s

ee9d924

Co-authored-by: FelixKrueger <FelixKrueger@users.noreply.github.com>

update bismark nf-test

b73a861

update tests for new assets/samplesheet

9866537

sateeshperi and others added 6 commits December 22, 2023 22:58

update snaps for sample name change

d95c82b

Merge pull request #362 from nf-core/no-groups

d447efa

No groups

Merge branch 'dev' into nf-core-template-merge-2.11.1

2086429

add test_data.config and update multiqc tests

774f267

update custom/dumpsoftwareversions module and snaps

f24bfb7

Merge pull request #368 from nf-core/nf-core-template-merge-2.11.1

f1ddce0

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

edmundmiller added this to the 2.6.0 milestone Jan 5, 2024

edmundmiller requested a review from sateeshperi January 5, 2024 18:27

edmundmiller self-assigned this Jan 5, 2024

edmundmiller requested a review from a team as a code owner January 5, 2024 18:27

chore: Bump versions for 2.6.0 release

0bc1575

edmundmiller force-pushed the dev branch from 86e0b55 to 0bc1575 Compare January 5, 2024 20:41

sateeshperi approved these changes Jan 5, 2024

View reviewed changes

edmundmiller enabled auto-merge January 5, 2024 21:17

FelixKrueger approved these changes Jan 5, 2024

View reviewed changes

edmundmiller merged commit 54f823e into master Jan 5, 2024
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Dev -> Master 2.6.0 #369

Dev -> Master 2.6.0 #369

edmundmiller commented Jan 5, 2024 •

edited

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github-actions bot commented Jan 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

sateeshperi commented Jan 5, 2024

FelixKrueger left a comment

Dev -> Master 2.6.0 #369

Dev -> Master 2.6.0 #369

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edmundmiller commented Jan 5, 2024 • edited Loading

github-actions bot commented Jan 5, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

sateeshperi commented Jan 5, 2024

FelixKrueger left a comment

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edmundmiller commented Jan 5, 2024 •

edited

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github-actions bot commented Jan 5, 2024 •

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