[pull] master from nf-core:master #10

pull · 2024-04-10T08:37:33Z

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Created by pull[bot]

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This reverts commit f5a1c41.

Important! Template update for nf-core/tools v2.11.1

fix vcf_collect when a tool is absent

… is not

Important! Template update for nf-core/tools v2.12

Merging 2.13.1

…vcf_fix2

Vcf fix2

…afusion into fix_rnaseqmetrics_mem

…s done

update collectrnaseqmetrics memory requirement

fix logical gate: when stringtie and not starfusion, only alignment i…

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

…ild_references, althought the main detection rnafusion analysis will not run

Release 3.0.2

github-actions · 2024-04-10T08:39:01Z

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

Posted for pipeline commit 42eb8d6

+| ✅ 166 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: 3.0.2
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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/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-rnafusion_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-rnafusion_logo_light.png
files_exist - File found: docs/images/nf-core-rnafusion_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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
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-rnafusion_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowRnafusion.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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.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 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 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.ensembl_version= 102
nextflow_config - Config default value correct: params.read_length= 100
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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
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
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/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/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 - assets/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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 badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (244 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.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' 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 a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-10 08:38:44

rannick and others added 30 commits December 19, 2023 13:34

fix vcf_collect when a tool is absent

f5a1c41

Template update for nf-core/tools version 2.11

266f007

Template update for nf-core/tools version 2.11.1

cfb0833

Merge branch 'dev' into nf-core-template-merge-2.11.1

683538f

Revert "fix vcf_collect when a tool is absent"

0ccea2e

This reverts commit f5a1c41.

fix vcf_collect when a tool is absent

d76dfc4

Merge branch 'dev' into nf-core-template-merge-2.11.1

b7b8c66

fix version issue

d163a4a

Merge pull request #457 from nf-core/nf-core-template-merge-2.11.1

81ded81

Important! Template update for nf-core/tools v2.11.1

Merge branch 'dev' into absent_tools

e996b93

prettier

81ca0c0

Template update for nf-core/tools version 2.12

d0f345a

update changelog

887624c

Merge pull request #458 from nf-core/absent_tools

ffe9c09

fix vcf_collect when a tool is absent

add dump and rewrite channel

901fa94

fix vcf_collect when fusioninspector output is empty but fusionreport…

c37fe98

… is not

update changelog

a6659da

update changelog

b67a751

Merge branch 'dev' into nf-core-template-merge-2.12

2dae239

black

26e492c

harmonise ensembl_version default to 102

b2db95e

prettier

30604e2

prettier with correct version

8c243b3

fix logos

239345a

fix editorconfig

49b2fb4

update logos from TEMPLATES

bc0e366

Merge pull request #464 from nf-core/nf-core-template-merge-2.12

d514957

Important! Template update for nf-core/tools v2.12

Merge branch 'dev' into fix_whitelist

6f7d915

Merge branch 'dev' into fix_vcf

017d6da

update changelog

066993e

rannick and others added 28 commits March 18, 2024 14:10

bugfix for vcf

a66ec84

Merge pull request #480 from nf-core/merging_2.13.1

5858c3c

Merging 2.13.1

Merge branch 'dev' into vcf_fix2

fa9e830

black without line limit

3ec3090

Merge branch 'vcf_fix2' of https://github.com/nf-core/rnafusion into …

2660469

…vcf_fix2

update changelog

2b6ff48

Merge pull request #481 from nf-core/vcf_fix2

fe3de40

Vcf fix2

merging

8f02765

align {

78a56b3

Merge branch 'fix_rnaseqmetrics_mem' of https://github.com/nf-core/rn…

2448d7f

…afusion into fix_rnaseqmetrics_mem

fix logical gate: when stringtie and not starfusion, only alignment i…

3ab9344

…s done

fix conda package requirements

6a36c3e

Merge pull request #474 from nf-core/fix_rnaseqmetrics_mem

4fe1a5d

update collectrnaseqmetrics memory requirement

update changelog

d506c69

Merge branch 'dev' into fix_stringtie_log_gate

88a3540

Merge pull request #482 from nf-core/fix_stringtie_log_gate

e50eed2

fix logical gate: when stringtie and not starfusion, only alignment i…

bump version 3.0.2

e3a909f

Merge branch 'master' into dev

86375ae

update changelog date

2dbd134

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

1f51050

remove emtpy file

58dd112

Update nextflow.config

a5428bf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

remove nf-test.log

3602cc0

Update workflows/rnafusion.nf

5adb521

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

use a real input as validation of the samplesheet occurs even with bu…

d09c5bb

…ild_references, althought the main detection rnafusion analysis will not run

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

f18fab7

final release date in changelog

c27117b

Merge pull request #483 from nf-core/dev

42eb8d6

Release 3.0.2

pull bot added the ⤵️ pull label Apr 10, 2024

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[pull] master from nf-core:master #10

[pull] master from nf-core:master #10

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github-actions bot commented Apr 10, 2024

❗ Test warnings:

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[pull] master from nf-core:master #10

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github-actions bot commented Apr 10, 2024

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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pull bot commented Apr 10, 2024 •

edited

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