fix bcftools mpileup #1109

FriederikeHanssen · 2023-06-15T07:27:39Z

PR checklist

github-actions · 2023-06-15T07:30:38Z

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

Posted for pipeline commit 2e2397d

+| ✅ 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: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: pytest-workflow_release.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 09:53:32

subworkflows/local/bam_variant_calling_mpileup/main.nf

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

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

tests/test_mpileup.yml

maxulysse · 2023-06-15T08:16:31Z

Close #1104 #1103 #1099 #835

How many issues are you closing with this one PR?

FriederikeHanssen · 2023-06-15T08:20:06Z

all of them, tbf 3 of them are the same thing

tests/test_mpileup.yml

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

fix bcftools mpileup

37be36d

FriederikeHanssen requested a review from maxulysse as a code owner June 15, 2023 07:27

FriederikeHanssen added 2 commits June 15, 2023 07:28

consolidate docs

59923eb

Update changelog

5213603

maxulysse and others added 2 commits June 15, 2023 09:33

Merge branch 'dev' into mpileup

f31d7e0

also fix annotation for mpileup

387f4f4

maxulysse reviewed Jun 15, 2023

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subworkflows/local/bam_variant_calling_mpileup/main.nf Outdated Show resolved Hide resolved

maxulysse approved these changes Jun 15, 2023

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FriederikeHanssen and others added 2 commits June 15, 2023 07:35

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>

maxulysse mentioned this pull request Jun 15, 2023

Release candidate 3.2.2 #1096

Merged

10 tasks

FriederikeHanssen commented Jun 15, 2023

View reviewed changes

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf Outdated Show resolved Hide resolved

FriederikeHanssen added 3 commits June 15, 2023 09:38

Update subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

4345074

fix more publishing issues with mpileup

fcd5b64

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

c190e9e

maxulysse approved these changes Jun 15, 2023

View reviewed changes

FriederikeHanssen commented Jun 15, 2023

View reviewed changes

tests/test_mpileup.yml Show resolved Hide resolved

Update tests/test_mpileup.yml

e3d80cf

variable md5sums

8fb0b53

maxulysse reviewed Jun 15, 2023

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tests/test_mpileup.yml Outdated Show resolved Hide resolved

Update tests/test_mpileup.yml

2e2397d

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

FriederikeHanssen merged commit 8e5bb2d into nf-core:dev Jun 15, 2023

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fix bcftools mpileup #1109

fix bcftools mpileup #1109

FriederikeHanssen commented Jun 15, 2023 •

edited

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github-actions bot commented Jun 15, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Jun 15, 2023

FriederikeHanssen commented Jun 15, 2023

fix bcftools mpileup #1109

fix bcftools mpileup #1109

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FriederikeHanssen commented Jun 15, 2023 • edited Loading

PR checklist

github-actions bot commented Jun 15, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Jun 15, 2023

FriederikeHanssen commented Jun 15, 2023

FriederikeHanssen commented Jun 15, 2023 •

edited

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github-actions bot commented Jun 15, 2023 •

edited

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