Prepare 3.0 release by maxulysse · Pull Request #631 · nf-core/sarek

maxulysse · 2022-07-13T10:46:53Z

PR checklist

github-actions · 2022-07-13T10:47:07Z

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

It looks like this pull-request is has been made against the maxulysse/nf-core_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 maxulysse/nf-core_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 · 2022-07-17T10:57:10Z

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

Posted for pipeline commit b9a891c

+| ✅ 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 14:16:29

…adding anything in our etup

Umi test

Nextflow_schema.json updates

nf-core modules update -a

PON not correctly validated

Simplify multiqc config channels

Fix --intervals false

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

add split fastq to test full

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

add cnvkit index

lescai

I've improved the documentation for UMI read structure. Thanks for the suggestions, it's not the simplest topic to explain in short.

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

fix path to file in csv files

Update comments merged on the 3.0 PR back to dev

SVDB MERGE update

maxulysse · 2022-07-20T13:27:38Z

Replaced by #672

maxulysse marked this pull request as draft July 13, 2022 10:56

maxulysse marked this pull request as ready for review July 14, 2022 09:18

maxulysse and others added 26 commits July 17, 2022 16:17

update skip_markduplicates tests

0150003

fix mosdepth

f1453a3

update umi checksums

e053000

no need to overwrite the dragmap prefix, it is the same

0e40b6a

remove checksum for collated bam file

eb07bf0

if reference is provided then no bed file

fb1e756

have freebayes only use a single core, parallel implementation isn't …

440d2f9

…adding anything in our etup

add warn if intervals is provided without wes

85afefc

combine conditionals

62e182e

fix pon validation

1411796

Merge pull request nf-core#614 from WackerO/umi

e8d484f

Umi test

Merge pull request nf-core#646 from FriederikeHanssen/params

5dc3f3b

Nextflow_schema.json updates

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

442d9b5

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

8b9183d

fix output

9194d97

fix output

3e7bdd8

Merge pull request nf-core#633 from maxulysse/dev_modules_update

5b83a5d

nf-core modules update -a

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

f4055c8

update aligner tests expected files

770881c

Add vague statement about md and bqsr

7600d62

Add comments about bwa parameters

3f1002e

add comment on empty snpeff plots in multiqc

0064a9c

Merge pull request nf-core#648 from FriederikeHanssen/param_valid

45aab1c

PON not correctly validated

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

ee4b556

fix output for targete bed

4ecd84e

code polish

c39047a

FriederikeHanssen and others added 18 commits July 20, 2022 10:23

remove task.ext.args that is not used in local module

7082782

Merge branch 'dev' into index_svg

2fd6afd

Updated SVDB module

081f8e2

Merge branch 'dev' of https://github.com/nf-core/sarek into svdb

c43ea10

Merge pull request nf-core#666 from SusiJo/multiqc_channels

d1402dd

Simplify multiqc config channels

Merge pull request nf-core#655 from FriederikeHanssen/intervals_fasta

3720676

Fix --intervals false

Update conf/modules.config

da917e1

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

Merge pull request nf-core#665 from ggabernet/fulltests

08f130b

add split fastq to test full

Update conf/modules.config

c48b7f1

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

Merge pull request nf-core#661 from FriederikeHanssen/index_svg

93a4925

add cnvkit index

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

c064aee

Merge branch '3.0' into dev_3.0_PR

db7024e

Updated module again

da6cfc9

Merge branch 'dev' of https://github.com/nf-core/sarek into svdb

d47bb26

Merge branch 'svdb' of https://github.com/WackerO/sarek into svdb

ba020b3

remove duplication

fc50739

fix path to file in csv files

335396a

update CHANGELOG

a36e697

lescai reviewed Jul 20, 2022

View reviewed changes

Comment thread docs/usage.md

maxulysse and others added 6 commits July 20, 2022 14:02

Apply suggestions from code review

fc09504

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

Updated test

b1ce5bb

Merge pull request nf-core#669 from maxulysse/dev_restart_csv

cff880f

fix path to file in csv files

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

23453e8

Merge pull request nf-core#664 from maxulysse/dev_3.0_PR

467b2e6

Update comments merged on the 3.0 PR back to dev

Merge pull request nf-core#667 from WackerO/svdb

3441df4

SVDB MERGE update

lescai reviewed Jul 20, 2022

View reviewed changes

Comment thread README.md

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

b9a891c

maxulysse closed this Jul 20, 2022

maxulysse deleted the 3.0 branch September 5, 2022 12:25

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Prepare 3.0 release#631

Prepare 3.0 release#631
maxulysse wants to merge 2632 commits intonf-core:masterfrom
maxulysse:3.0

maxulysse commented Jul 13, 2022

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github-actions Bot commented Jul 17, 2022 •

edited

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❗ Test warnings:

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✅ Tests passed:

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maxulysse commented Jul 20, 2022

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maxulysse commented Jul 13, 2022

PR checklist

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github-actions Bot commented Jul 13, 2022

This PR is against the master branch ❌

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Jul 20, 2022

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This PR is against the `master` branch ❌

github-actions Bot commented Jul 17, 2022 •

edited

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