Add variant caller to bcftools/vcftools + multiqc by SusiJo · Pull Request #618 · nf-core/sarek

SusiJo · 2022-07-05T06:56:27Z

Also close #621

PR checklist

This PR fixes the sample names of the files in results/reports/bcftools, results/reports/vcftools and results/multiqc and adds the variant caller to the sample name.

github-actions · 2022-07-05T06:58:05Z

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

Posted for pipeline commit 43a0a52

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

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

✅ 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: .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/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-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 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: .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.version
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 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 manifest.version ends in dev: '3.0dev'
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 - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore 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 in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (383 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
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
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: local_modules.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.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'.

Run details

nf-core/tools version 2.4.1
Run at 2022-07-14 08:26:38

maxulysse · 2022-07-11T16:23:00Z

Is this PR closing this one too: #526

SusiJo · 2022-07-13T14:24:25Z

Still need to remove uncommented stuff and some dump statements. But most of it can be reviewed already.
Especially the prefixes in the modules.config should be reviewed cautiously. Hope I'm not introducing any new bugs that the tests do not cover.

SusiJo · 2022-07-13T14:26:03Z

This should also fix the null folder of tiddit and issues related to targets.bed.

maxulysse

Just minor comments.
Amazing job, love it

SusiJo · 2022-07-13T14:48:11Z

Thanks @maxulysse for reviewing!

FriederikeHanssen

great work, I can take a more detailed look still if you want, but looks really good

FriederikeHanssen · 2022-07-14T06:46:30Z

@SusiJo since these are quite significant changes did you also run the mnaul tests locally?

SusiJo · 2022-07-14T06:52:19Z

Yes, i ran almost all test cases locally, including all manual tests. I'm just wondering about strelkakb with manta and strelka together. Before applying the prefix changes, the strelka was using the manta output. Now both produce outputs 🤔

FriederikeHanssen · 2022-07-14T08:05:08Z

The PR looks almost ready to be merged. I couldn’t find anything obvious.

SusiJo added 2 commits July 5, 2022 06:49

add variant calling tool to vcf/bcftools + multiqc

2613281

Merge remote-tracking branch 'origin/dev' into bcftools_vcftools

51b6cc6

SusiJo added 4 commits July 6, 2022 14:30

fix vcftools + fix typos

1e6704c

Merge remote-tracking branch 'origin/dev' into bcftools_vcftools

2f21bcc

fix mutect + gender

173f7b6

update multiqc module

71901f2

maxulysse mentioned this pull request Jul 13, 2022

TIDDIT output folder named null #621

Closed

SusiJo added 6 commits July 13, 2022 10:49

update outputs varcallers + ci tests

4e30625

Merge remote-tracking branch 'origin/dev' into bcftools_vcftools

dcfd6cf

update ymls

2c2cbdb

update ymls

a4b21dc

update yml

2f966b4

update ascat yml

1992894

SusiJo marked this pull request as ready for review July 13, 2022 14:39

SusiJo requested a review from maxulysse as a code owner July 13, 2022 14:39

SusiJo requested a review from FriederikeHanssen July 13, 2022 14:40

maxulysse reviewed Jul 13, 2022

View reviewed changes

Comment thread conf/modules.config

maxulysse reviewed Jul 13, 2022

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Comment thread workflows/sarek.nf Outdated

maxulysse reviewed Jul 13, 2022

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Comment thread workflows/sarek.nf Outdated

maxulysse reviewed Jul 13, 2022

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FriederikeHanssen reviewed Jul 13, 2022

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Comment thread assets/multiqc_config.yml Outdated

FriederikeHanssen approved these changes Jul 13, 2022

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Comment thread workflows/sarek.nf Outdated

Comment thread tests/test_tools_manually.yml

add suggested changes + rm view/dumps

4a5ed75

SusiJo added 3 commits July 14, 2022 07:08

Merge remote-tracking branch 'origin/dev' into bcftools_vcftools

b952b6e

revert back to former multiqc_config

e750e4e

add description schema description for ascat

558ecd3

FriederikeHanssen reviewed Jul 14, 2022

View reviewed changes

Comment thread conf/modules.config Outdated

rm unnecessary ext.args for multiqc

43a0a52

maxulysse approved these changes Jul 14, 2022

View reviewed changes

maxulysse merged commit 5949d5f into nf-core:dev Jul 14, 2022

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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SusiJo commented Jul 5, 2022 •

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

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