Review Comments for release by FriederikeHanssen · Pull Request #660 · nf-core/sarek

FriederikeHanssen · 2022-07-19T13:57:38Z

… ifEmpty for reports

PR checklist

… ifEmpty for reports

github-actions · 2022-07-19T14:16:38Z

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

Posted for pipeline commit 6a893cc

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
schema_description - No description provided in schema for parameter: ascat_ploidy

❔ 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 (372 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: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest_somatic.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.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'.

Run details

nf-core/tools version 2.4.1
Run at 2022-07-20 15:08:56

SusiJo

Looking good!! 🚀

comment nextflow config, meta map readability, add ch_ prefix, remove…

8db1809

… ifEmpty for reports

FriederikeHanssen added 16 commits July 19, 2022 16:43

Add missing , after refactor

15949f5

also indent the meta values for prettiness

46b7c2c

remove individual subworkflow tests for now

763f85d

add split() to all tools calls

0902fa0

fix syntax

46ff17e

remove local subworkflow testing since it is ot run

6e6d352

indents

68498a1

indent subworkflow calls more consistently

b51279b

add more line breaks & clarify magic booleans

3b8d92e

remove unneeded vep_cache version

c4e8a39

remove genome, using default

b0024ef

formatting

d55d37d

merge upstream/dev

2b20ebf

fix channel naming after merge

13b71d8

remove trimgalore wf, we are not using it anymore

be4b2a3

add refactor deleted channel back

fb0278f

maxulysse approved these changes Jul 20, 2022

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SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/variantcalling/manta/somatic/main.nf

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf

merge upstream/dev

039f236

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf Outdated

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf

sort meta fields alphabetically where missing

0a65271

SusiJo reviewed Jul 20, 2022

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Comment thread subworkflows/nf-core/variantcalling/tiddit/main.nf Outdated

FriederikeHanssen added 2 commits July 20, 2022 12:55

sort meta fields alphabetically where missing

d73b835

harmonize tiddit file structure

28e88fa

FriederikeHanssen marked this pull request as ready for review July 20, 2022 11:04

maxulysse approved these changes Jul 20, 2022

View reviewed changes

address umi concerns & docs

153bcd0

FriederikeHanssen mentioned this pull request Jul 20, 2022

Prepare 3.0 release #631

Closed

11 tasks

SusiJo reviewed Jul 20, 2022

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Comment thread workflows/sarek.nf

SusiJo approved these changes Jul 20, 2022

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FriederikeHanssen added 5 commits July 20, 2022 15:06

add ifempty([]) in case ch_reports contains nothing

2632a7b

Merge remote-tracking branch 'upstream/dev' into release_review

de5ad1a

umis need to be passed properly

0e60f16

merge upstream/dev

10cd8a2

merge upstream/dev

6a893cc

FriederikeHanssen merged commit 6f41b7c into nf-core:dev Jul 20, 2022

FriederikeHanssen deleted the release_review branch July 10, 2023 19:01

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Review Comments for release#660

Review Comments for release#660
FriederikeHanssen merged 27 commits intonf-core:devfrom
FriederikeHanssen:release_review

FriederikeHanssen commented Jul 19, 2022

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github-actions Bot commented Jul 19, 2022 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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FriederikeHanssen commented Jul 19, 2022

PR checklist

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github-actions Bot commented Jul 19, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions Bot commented Jul 19, 2022 •

edited

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