Release 3.0.0 - three kings #181

Lucpen · 2024-11-07T15:44:13Z

PR checklist

…tomte into drop_db

Merge pull request #157 from genomic-medicine-sweden/dev

…s_and_vep Update vep to 112 and references encode 46

Add documentation

bump to version 3.0.0

github-actions · 2024-11-07T15:46:19Z

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

Posted for pipeline commit 2963ecb

+| ✅ 182 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-tomte_logo_light.png
files_exist - File is ignored: docs/images/nf-core-tomte_logo_light.png
files_exist - File is ignored: docs/images/nf-core-tomte_logo_dark.png
files_exist - File is ignored: docs/images/tomte_logo.eps
files_exist - File is ignored: docs/images/tomte_pipeline_metromap.svg
files_exist - File is ignored: docs/images/tomte_pipeline_metromap.png
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-tomte_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/tomte/tomte/.github/workflows/awstest.yml
modules_config - modules_config

✅ 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: 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/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: conf/test.config
files_exist - File found: conf/test_full.config
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: 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: conf/igenomes_ignored.config
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-tomte_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowTomte.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: 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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 3.0.0
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= results
nextflow_config - Config default value correct: params.save_mapped_as_cram= true
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.gencode_annotation_version= 46
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.platform= illumina
nextflow_config - Config default value correct: params.save_reference= true
nextflow_config - Config default value correct: params.vep_cache_version= 112
nextflow_config - Config default value correct: params.skip_download_vep= true
nextflow_config - Config default value correct: params.skip_download_gnomad= true
nextflow_config - Config default value correct: params.min_trimmed_length= 40
nextflow_config - Config default value correct: params.star_two_pass_mode= Basic
nextflow_config - Config default value correct: params.skip_subsample_region= false
nextflow_config - Config default value correct: params.skip_downsample= false
nextflow_config - Config default value correct: params.seed_frac= 0.001
nextflow_config - Config default value correct: params.num_reads= 120000000
nextflow_config - Config default value correct: params.variant_caller= bcftools
nextflow_config - Config default value correct: params.bcftools_caller_mode= multiallelic
nextflow_config - Config default value correct: params.skip_variant_calling= false
nextflow_config - Config default value correct: params.skip_build_tracks= false
nextflow_config - Config default value correct: params.skip_stringtie= false
nextflow_config - Config default value correct: params.skip_vep= false
nextflow_config - Config default value correct: params.skip_drop_ae= false
nextflow_config - Config default value correct: params.skip_drop_as= false
nextflow_config - Config default value correct: params.skip_export_counts_drop= true
nextflow_config - Config default value correct: params.drop_group_samples_ae= outrider
nextflow_config - Config default value correct: params.drop_group_samples_as= fraser
nextflow_config - Config default value correct: params.drop_padjcutoff_ae= 0.05
nextflow_config - Config default value correct: params.drop_padjcutoff_as= 0.1
nextflow_config - Config default value correct: params.drop_zscorecutoff= 0.0
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/raredisease
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.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 found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-11-18 06:49:33

Lucpen · 2024-11-08T10:03:34Z

Hi guys, I want to have the release ASAP but I am having some issues with the download test. As all the other tests pass, I think this issue is likely related to the fact that the pull_request_target runs with the code from the PR target, what do you guys think? @fellen31 @jemten @ramprasadn

jemten

Ready for holiday season 🎄 👑

fellen31 · 2024-11-11T09:51:16Z

Hi guys, I want to have the release ASAP but I am having some issues with the download test. As all the other tests pass, I think this issue is likely related to the fact that the pull_request_target runs with the code from the PR target, what do you guys think? @fellen31 @jemten @ramprasadn

Downloading the pipeline seems works fine for me locally. Perhaps something with the action.

fix bug running variant calling gatk and fix dev bug in bcf norm

Co-authored-by: Felix Lenner <[email protected]>

…g_variant_caller change way of adding variant caller to vcf

CHANGELOG.md

Merge pull request #181 from genomic-medicine-sweden/dev

Lucpen and others added 30 commits July 30, 2024 13:48

feat add make database

e9fbca1

fix linting

c1d5a49

Merge branch 'dev' into drop_db

a4234de

Merge branch 'dev' into drop_db

4b33ba8

Prevent module skipping if no annotation or counts provided

3ef078b

Merge branch 'drop_db' of https://github.com/genomic-medicine-sweden/…

1a45b7a

…tomte into drop_db

Merge branch 'dev' into drop_db

3e7a463

Merge branch 'dev' into drop_db

28c623a

Merge branch 'dev' into drop_db

983f0ae

Merge pull request #158 from genomic-medicine-sweden/master

6e00503

Merge pull request #157 from genomic-medicine-sweden/dev

Merge branch 'dev' into drop_db

c43a8f7

update DROP and fix drop_config

994147f

update vep

54852f2

update gencode version to 46

c906ca3

CHANGELOG

570cf67

Merge pull request #159 from genomic-medicine-sweden/update_reference…

9e3cb47

…s_and_vep Update vep to 112 and references encode 46

Merge branch 'dev' into drop_db

3318ad0

fix CHANGELOG

9556308

fix CHANGELOG

afffbb1

run prettier

52dbc7a

update clinvar version

19a2435

add count mode and overlap to sampan

f3d2d0c

Update conf/base.config

28e537f

Lund updates to the drop_db branch

26907b1

Correct ignoring of exported counts

2e4ef93

mkdir -p

f0d68ff

Update modules/local/drop_config_runAE.nf

ba154d2

Update modules/local/drop_config_runAS.nf

aeaf98b

Update modules/local/drop_config_runAE.nf

3d1beaa

Update modules/local/drop_config_runAE.nf

694d5e6

Lucpen and others added 3 commits November 7, 2024 12:45

Merge pull request #178 from genomic-medicine-sweden/documentation

539a034

Add documentation

bump version

0fbfae5

Merge pull request #180 from genomic-medicine-sweden/prepare_release

3ffe8b8

bump to version 3.0.0

Lucpen requested a review from a team as a code owner November 7, 2024 15:44

Lucpen added the Ready for review Ready for review label Nov 8, 2024

jemten approved these changes Nov 11, 2024

View reviewed changes

Lucpen and others added 17 commits November 12, 2024 16:44

fix bcf norm

be84ae9

line end

07c6832

fix bug

a3488a4

Update CHANGELOG.md

e2bd5e7

prettier

dd179c7

Merge pull request #182 from genomic-medicine-sweden/fix_bcf_norm

dce594f

fix bug running variant calling gatk and fix dev bug in bcf norm

change_way_adding_variant_caller to vcf

bb538df

Update CHANGELOG.md

b05a59e

remove foundin.hdr

69992ca

fix

a4b1d87

fix

23cceae

Update CHANGELOG.md

3cf3f72

Update CHANGELOG.md

a9605f0

Co-authored-by: Felix Lenner <[email protected]>

remove bcftools/annotate

2728eb6

change

34837f9

prettier

1c70ea4

Merge pull request #184 from genomic-medicine-sweden/change_way_addin…

c23b4b8

…g_variant_caller change way of adding variant caller to vcf

Lucpen commented Nov 18, 2024

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

2963ecb

Lucpen merged commit 80f7fc8 into master Nov 18, 2024
27 of 29 checks passed

Lucpen added a commit that referenced this pull request Nov 18, 2024

Merge pull request #185 from genomic-medicine-sweden/master

811ff83

Merge pull request #181 from genomic-medicine-sweden/dev

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Release 3.0.0 - three kings #181

Release 3.0.0 - three kings #181

Lucpen commented Nov 7, 2024

github-actions bot commented Nov 7, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Lucpen commented Nov 8, 2024

jemten left a comment

fellen31 commented Nov 11, 2024

Release 3.0.0 - three kings #181

Release 3.0.0 - three kings #181

Conversation

Lucpen commented Nov 7, 2024

PR checklist

github-actions bot commented Nov 7, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Lucpen commented Nov 8, 2024

jemten left a comment

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fellen31 commented Nov 11, 2024

github-actions bot commented Nov 7, 2024 •

edited

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