Update comments merged on the 3.0 PR back to dev by maxulysse · Pull Request #664 · nf-core/sarek

maxulysse · 2022-07-20T07:52:59Z

PR checklist

Prepare release 2.7.1

…e/issue-555/caching-bugfix Fix `MapReads` caching bug

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

maxulysse · 2022-07-20T08:04:43Z

Do not merge this one, let's keep it, until we're ready to merge #631
Merge this one first, sync #631 and merge, and release

SusiJo

Looking good 👍

FriederikeHanssen

approving, just the usage.md needs the duplicate sections removed

github-actions · 2022-07-20T10:52:06Z

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

Posted for pipeline commit fc09504

+| ✅ 146 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 (385 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: local_modules.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 12:22:00

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

maxulysse and others added 30 commits May 13, 2021 16:40

feat: nf-core bump-version . 2.7.1

546ccd3

feat: manual bump to 2.7.1

168b918

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

3230b99

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

b3f1fa5

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

ec59f4f

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

4952831

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

ba8eed5

Merge remote-tracking branch 'upstream/dev' into dev_2.7.1

3c98945

Merge pull request nf-core#374 from maxulysse/dev_2.7.1

68b9930

Prepare release 2.7.1

Fix MapReads caching bug (nf-core#555)

48960d4

Bump version to 2.7.2

613193e

Ensure DSL1 is used

0842a51

Update Sarek workflow PNG image

1e71ee3

Merge pull request nf-core#566 from Sage-Bionetworks-Workflows/bgrand…

e8f56e5

…e/issue-555/caching-bugfix Fix `MapReads` caching bug

Merge remote-tracking branch 'upstream/dev' into 3.0

784ea35

Merge remote-tracking branch 'upstream/dev' into 3.0

3b68cb2

Merge remote-tracking branch 'upstream/dev' into 3.0

ccf33f6

prettier

1dbb717

Merge remote-tracking branch 'upstream/dev' into 3.0

22d3b44

Merge remote-tracking branch 'upstream/dev' into 3.0

8b9183d

Merge remote-tracking branch 'upstream/dev' into 3.0

f4055c8

Merge remote-tracking branch 'upstream/dev' into 3.0

0261cd0

Merge remote-tracking branch 'upstream/dev' into 3.0

813a5cb

Merge remote-tracking branch 'upstream/dev' into 3.0

b1068e3

Merge remote-tracking branch 'upstream/dev' into 3.0

7c3bcfc

Update workflows/sarek.nf

980f76b

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

Merge remote-tracking branch 'upstream/dev' into 3.0

5556e57

Merge branch '3.0' of github.com:maxulysse/nf-core_sarek into 3.0

433ef65

Update README.md

a958da4

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>

Update README.md

0c0a83e

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

FriederikeHanssen and others added 6 commits July 19, 2022 19:59

Update README.md

bb9a013

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

Update docs/usage.md

3142264

Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

Apply suggestions from code review

0264d84

Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

Merge remote-tracking branch 'upstream/dev' into 3.0

5271e35

Merge branch '3.0' of github.com:maxulysse/nf-core_sarek into 3.0

b58ca44

Merge branch '3.0' into dev

11c1842

FriederikeHanssen reviewed Jul 20, 2022

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Merge remote-tracking branch 'upstream/dev' into 3.0

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SusiJo reviewed Jul 20, 2022

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maxulysse added 2 commits July 20, 2022 12:38

Merge remote-tracking branch 'upstream/dev' into 3.0

c064aee

Merge branch '3.0' into dev_3.0_PR

db7024e

FriederikeHanssen approved these changes Jul 20, 2022

View reviewed changes

remove duplication

fc50739

asp8200 reviewed Jul 20, 2022

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maxulysse commented Jul 20, 2022

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Apply suggestions from code review

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

asp8200 approved these changes Jul 20, 2022

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maxulysse merged commit 467b2e6 into nf-core:dev Jul 20, 2022

maxulysse deleted the dev_3.0_PR branch July 20, 2022 13:06

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Update comments merged on the 3.0 PR back to dev#664

Update comments merged on the 3.0 PR back to dev#664
maxulysse merged 41 commits intonf-core:devfrom
maxulysse:dev_3.0_PR

maxulysse commented Jul 20, 2022

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github-actions Bot commented Jul 20, 2022 •

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maxulysse commented Jul 20, 2022

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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github-actions Bot commented Jul 20, 2022 •

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