Release candidate 3.2.2 #1096

maxulysse · 2023-06-12T09:22:26Z

Need:

CHORES: Prepare 3.2.2 #1095

Would be nice with

FIX: Fix default memory issue with gatk4/createsequencedictionary

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>

…test_cache

FIX: Remove duplicated code

FEATURE: Non hidden files with -profile test

…t_file to baseName. Apparently needed to get the manuael ascat test working.

Fix ascat manual test

github-actions · 2023-06-12T09:24:37Z

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

Posted for pipeline commit 702e3bc

+| ✅ 153 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '3.2.2'

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
template_strings - template_strings

✅ 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-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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/WorkflowSarek.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-sarek_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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
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: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: pytest-workflow_release.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 2023-06-15 12:39:51

CHORES: Prepare 3.2.2

FIX: Mutect2 subworkflow

update config

Co-authored-by: Robert Syme <rob.syme@gmail.com>

FIX: Refactor prefix definition

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>

.github/workflows/pytest-workflow_release.yml

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>

fix bcftools mpileup

FriederikeHanssen

not a good person to approve, but lgtm

.github/workflows/pytest-workflow_release.yml

.github/workflows/ci.yml

asp8200

LGTM - except for the failing tests due to exceeded API rate limit.

maxulysse and others added 23 commits June 9, 2023 11:45

FIX: gatk4/createsequencedictionary default memory

e79b306

update CHANGELOG

7cf95fe

remove md5checksum

ecf8e72

Merge pull request #1087 from maxulysse/new_dev

5c2017d

FIX: Fix default memory issue with gatk4/createsequencedictionary

replace test by test_cache and add test with non obfuscated files

01119fe

Merge branch 'dev' into test_cache

641cdbc

update CHANGELOG

ab8ced4

test only on docker

162ac72

test with singularity and conda when PR on master

1f40c3d

Apply suggestions from code review

51a3ede

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>

Update .github/workflows/pytest-workflow_release.yml

c19188e

update usage

4d0a5f3

Merge branch 'test_cache' of github.com:maxulysse/nf-core_sarek into …

67c1186

…test_cache

remove duplicated code

51ac097

update CHANGELOG

3a4a7f8

update CHANGELOG

7fcf0fc

Merge pull request #1089 from maxulysse/duplication

bce4a4c

FIX: Remove duplicated code

Merge pull request #1088 from maxulysse/test_cache

5c45e5c

FEATURE: Non hidden files with -profile test

Reverting meta.id in channels allele_files, loci_files, gc_file and r…

7b10235

…t_file to baseName. Apparently needed to get the manuael ascat test working.

Merge branch 'dev' into fix_ascat_manual_test

f238efa

Updating changelog

c3eb660

Merge pull request #1093 from nf-core/fix_ascat_manual_test

ecb49a8

Fix ascat manual test

prepare 3.2.2

fbe6059

maxulysse and others added 6 commits June 12, 2023 12:46

Update CHANGELOG.md

f5389b6

Merge pull request #1095 from maxulysse/prepare_release-3.2.2

3dce752

CHORES: Prepare 3.2.2

fix Mutect2 subworkflow bug

b9030ff

remove duplicate index for deepvariant when no_intervals

15909a4

update CHANGELOG

66ce8e8

Merge pull request #1098 from maxulysse/fix_mutect2_subworkflow

400b4ae

FIX: Mutect2 subworkflow

maxulysse and others added 15 commits June 14, 2023 13:14

update CHANGELOG

6ead4a9

Merge pull request #1107 from maxulysse/public_aws_ecr_singularity

875faee

update config

refactor prefix definition for vcf files

91c8c89

baseName, not name

806f3d6

Update conf/modules/joint_germline.config

febf7d8

Co-authored-by: Robert Syme <rob.syme@gmail.com>

variant_file not vcf

6276707

Merge pull request #1108 from maxulysse/remove_minus

abc7fe6

FIX: Refactor prefix definition

fix bcftools mpileup

37be36d

consolidate docs

59923eb

Update changelog

5213603

Merge branch 'dev' into mpileup

f31d7e0

also fix annotation for mpileup

387f4f4

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

b7b1655

Update subworkflows/local/bam_variant_calling_mpileup/main.nf

0ed285e

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>

Update subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

4345074

maxulysse commented Jun 15, 2023

View reviewed changes

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maxulysse and others added 7 commits June 15, 2023 09:42

Update .github/workflows/pytest-workflow_release.yml

62aa7ee

fix more publishing issues with mpileup

fcd5b64

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

c190e9e

Update tests/test_mpileup.yml

e3d80cf

variable md5sums

8fb0b53

Update tests/test_mpileup.yml

2e2397d

Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>

Merge pull request #1109 from FriederikeHanssen/mpileup

8e5bb2d

fix bcftools mpileup

FriederikeHanssen approved these changes Jun 15, 2023

View reviewed changes

maxulysse commented Jun 15, 2023

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maxulysse commented Jun 15, 2023

View reviewed changes

.github/workflows/pytest-workflow_release.yml Outdated Show resolved Hide resolved

Apply suggestions from code review

702e3bc

asp8200 reviewed Jun 15, 2023

View reviewed changes

.github/workflows/ci.yml Show resolved Hide resolved

asp8200 approved these changes Jun 15, 2023

View reviewed changes

asp8200 merged commit 6ec8c1c into master Jun 15, 2023

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Release candidate 3.2.2 #1096

Release candidate 3.2.2 #1096

maxulysse commented Jun 12, 2023 •

edited by FriederikeHanssen

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github-actions bot commented Jun 12, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

FriederikeHanssen left a comment

asp8200 left a comment •

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Release candidate 3.2.2 #1096

Release candidate 3.2.2 #1096

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maxulysse commented Jun 12, 2023 • edited by FriederikeHanssen Loading

github-actions bot commented Jun 12, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

FriederikeHanssen left a comment

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maxulysse commented Jun 12, 2023 •

edited by FriederikeHanssen

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github-actions bot commented Jun 12, 2023 •

edited

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

asp8200 left a comment •

edited

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