[DON' MERGE] Release 3.4.0 #1320

FriederikeHanssen · 2023-11-08T12:50:42Z

PR checklist

…e_pcr_indel_model

…f-core#1210

…t-valling with Dnascope

…alling with Sentieon Dnascope

…t_genemetrics

…ant-calling

…plotyper_joint_germline

…nd genotype_tbi. (Needed for output csv-file.)

…rmline.yml

…ermline.yml

Co-authored-by: Maxime U Garcia <[email protected]>

Bump version, set release names

github-actions · 2023-11-08T12:50:54Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @FriederikeHanssen,

It looks like this pull-request is has been made against the FriederikeHanssen/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the FriederikeHanssen/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2023-11-08T12:58:18Z

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

Posted for pipeline commit b9ee3fe

+| ✅ 143 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.4.0
pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
schema_description - No description provided in schema for parameter: bcftools_annotations
schema_description - No description provided in schema for parameter: bcftools_annotations_index
schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/modules.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/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_ci - actions_ci
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: conf/test.config
files_exist - File found: conf/test_full.config
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/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: 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: 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-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.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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
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
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: branch.yml
actions_schema_validation - Workflow validation passed: release-announcments.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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 2023-11-08 12:52:18

maxulysse

Looking good

conf/test/cache.config

workflows/sarek.nf

subworkflows/local/samplesheet_to_channel/main.nf

mirpedrol

LGTM

CHANGELOG.md

subworkflows/local/samplesheet_to_channel/main.nf

maxulysse · 2023-11-08T14:10:29Z

PR should be from dev to master, not your branch

maxulysse · 2023-11-08T14:13:52Z

PR should be from dev to master, not your branch

I think it'll be good to have the sentieon tests for the release

FriederikeHanssen · 2023-11-08T14:18:04Z

PR should be from dev to master, not your branch

🤦‍♀️ will open a new PR, but keep this one since people started reviewing it.

FriederikeHanssen · 2023-11-09T08:40:21Z

Reviews addressed in #1324 . Will close this PR and merge reviews into dev. This PR is superseded by #1321

Address code reviews from #1320

asp8200 and others added 30 commits August 28, 2023 12:33

align

4dcdc9c

Changing Sarek-option sentieon_dnascope_pcr_based to sentieon_dnascop…

cec591b

…e_pcr_indel_model

Adding meta to some input-channels for Dnascope module

b2fbd53

Updated dnascope

c12ce59

Adding option dnascope_filter for skip_tools. Will be removed later n…

47ec913

…f-core#1210

Add variant-filter for DNASCOPE

79bf941

Trying to order stuff alphabetically

5aa33fb

calling BAM_JOINT_CALLING_GERMLINE_SENTIEON for joint-germline varian…

d8a06bd

…t-valling with Dnascope

Skipping Sentieon VarCal and ApplyVarCal for joint-germline variant-c…

56f65d6

…alling with Sentieon Dnascope

Merge branch 'dev' into sentieon_dnascope

7da3dec

Adding sentieon Dnascope to some error msgs and warnings

01562e7

adding gene metrics module

0e97157

updating documentation

cd43d53

updating changelog

e06866a

Merge branch 'dev' of https://github.com/grantn5/sarek into add_cnvki…

050df8e

…t_genemetrics

removing extra line from changelog

5ec2ff3

resolving conflicts from merging dev

f30048d

params.joint_germline was unintentionally out-commented

0f4080c

Continued implementing Sentieon Dnascope

cc72786

Fixing name of pytest. Replacing problematic ampersand character

5cf6520

Bug fix: Sent tbi to vcf-channel and vcf to tbi-channel

ccdf4e5

Adding a bit of error-handling for sentieon-based joint-germline vari…

d74ec55

…ant-calling

Separate configs for sentieon_dnascope_joint_germline and sentieon_ha…

a367e37

…plotyper_joint_germline

Adding tests for dnascope (excel joint-germline)

f55c22e

Adding meta tags patient and variantcaller to channels genotype_vcf a…

a10ad13

…nd genotype_tbi. (Needed for output csv-file.)

joint germline with dnascope

6c78764

test_sentieon_joint_germline.yml -> test_sentieon_haplotyper_joint_ge…

c48f68c

…rmline.yml

Adding test for joint-germline with dnascope

af59cd3

test_sentieon_joint_germline.yml -> test_sentieon_haplotyper_joint_g…

d0bb50d

…ermline.yml

initializing output channel gvcf_sentieon_dnascope

a063f3f

FriederikeHanssen and others added 12 commits November 8, 2023 10:38

bump version

c3145cc

set release name

6e3c1ca

fixz accidental overwrite

9f84559

fixz accidental overwrite

ee96200

Update CHANGELOG.md

83126c6

Update CHANGELOG.md

9bd8935

Co-authored-by: Maxime U Garcia <[email protected]>

Update CHANGELOG.md

063f51b

Update CHANGELOG.md

69599e2

using all position in the version

a9f26d2

using all position in the version

23dd300

using all position in the version

990571a

Merge pull request nf-core#1319 from FriederikeHanssen/prepare_release34

b9ee3fe

Bump version, set release names

FriederikeHanssen requested a review from maxulysse as a code owner November 8, 2023 12:50