Release 3.0.2 #483

rannick · 2024-04-03T14:07:21Z

PR checklist

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

…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…

github-actions · 2024-04-03T14:08:49Z

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

Posted for pipeline commit c27117b

+| ✅ 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 08:15:40

fevac

lgtm ⭐

512

fellen31

Looks good to me!

.nf-test.log

nextflow.config

subworkflows/local/fusioninspector_workflow.nf

workflows/rnafusion.nf

peterpru

Looks good to me 👍

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

workflows/rnafusion.nf

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

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

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 added 14 commits March 19, 2024 13:43

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

rannick added 2 commits April 3, 2024 16:18

update changelog date

2dbd134

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

1f51050

fevac approved these changes Apr 8, 2024

View reviewed changes

512 Outdated Show resolved Hide resolved

remove emtpy file

58dd112

rannick self-assigned this Apr 8, 2024

fellen31 approved these changes Apr 8, 2024

View reviewed changes

peterpru approved these changes Apr 8, 2024

View reviewed changes

Update nextflow.config

a5428bf

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

fellen31 reviewed Apr 8, 2024

View reviewed changes

workflows/rnafusion.nf Show resolved Hide resolved

rannick and others added 5 commits April 8, 2024 16:49

remove nf-test.log

3602cc0

Update workflows/rnafusion.nf

5adb521

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

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

rannick merged commit 42eb8d6 into master Apr 10, 2024
13 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 3.0.2 #483

Release 3.0.2 #483

rannick commented Apr 3, 2024

github-actions bot commented Apr 3, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fevac left a comment

fellen31 left a comment

peterpru left a comment

Release 3.0.2 #483

Release 3.0.2 #483

Conversation

rannick commented Apr 3, 2024

PR checklist

github-actions bot commented Apr 3, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fevac left a comment

Choose a reason for hiding this comment

fellen31 left a comment

Choose a reason for hiding this comment

peterpru left a comment

Choose a reason for hiding this comment

github-actions bot commented Apr 3, 2024 •

edited

Loading

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