Release 2.4.0 #400

rannick · 2023-09-13T15:02:44Z

PR checklist

Fix trim tail for reverse reads

This reverts commit 98fb0ba.

change(config) use institutional config by default

fix(fusionreport) set html as optional

Megafusion key error fix

update intro and usage documentation

Update filenames

update version number and changelog release formatting

github-actions · 2023-09-13T15:04:32Z

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

Posted for pipeline commit 3d24c12

+| ✅ 156 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: 2.4.0

✅ 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: 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: lib/nfcore_external_java_deps.jar
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowRnafusion.groovy
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: .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: .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
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 - 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 - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy 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
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (193 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: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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' 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 2.9
Run at 2023-09-22 06:55:06

tower.yml

…mentation

Co-authored-by: Vadym <[email protected]>

add descriptions of report files in tower.yml and correct output docu…

Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases

maxulysse · 2023-09-18T15:22:55Z

The pipeline institutional config file is now commented out, we should not be doing that: https://github.com/nf-core/rnafusion/blame/dev/nextflow.config#L144

no need to have the igenomes.config as well I believe

apeltzer · 2023-09-19T13:43:27Z

iGenomes was the only thing I could find, apart from what @maxulysse already mentioned. All other looks good 👍🏻

… merging)

nf-core-bot and others added 30 commits April 28, 2023 14:26

Template update for nf-core/tools version 2.8

8129fe7

Template update for nf-core/tools version 2.9

1867373

merging template 2.9

0837650

merging template 2.9

5aa1731

update modules

5778ee6

version bump

7e2772d

add meta info to references in modules

ef98ac9

remove igenome usage

640c122

Add trim tail for reverse reads

dd3772f

update changelog

5aeb727

prettier

9630917

optional html for fusionreport

90c120b

Merge pull request #379 from nf-core/fix_trim_tail_reverse

16ae4ef

Fix trim tail for reverse reads

Merge branch 'dev' into fix_fusionreport_optional_html

5b7dfc8

update changelog

88d1051

use institutional configs by default

fbf1c2e

update changelog

4c277dd

make fusioninspector tsv optional

98fb0ba

Revert "make fusioninspector tsv optional"

1db0246

This reverts commit 98fb0ba.

Merge pull request #381 from nf-core/default_institutional_config

a978a80

change(config) use institutional config by default

Merge branch 'dev' into fix_fusionreport_optional_html

5c84661

Merge pull request #380 from nf-core/fix_fusionreport_optional_html

ea2b723

fix(fusionreport) set html as optional

fix for megafusion key error

dffeb11

fix to allow other remote URI paths

4404ca1

Merge branch 'dev' into megafusion_key_error_fix

606d579

Merge branch 'dev' into cloud_path_fix

ec61075

Merge pull request #382 from efgstone/megafusion_key_error_fix

2023c40

Megafusion key error fix

update modules

0699dca

bump version

3d31b27

Merge branch 'dev' into nf-core-template-merge-2.9

6ee0bfa

rannick added 10 commits September 13, 2023 15:14

Merge pull request #396 from nf-core/update_documentation

2bfdb59

update intro and usage documentation

Merge branch 'dev' into update_filenames

9e57ee3

add missing fusionreport stub and changelog update for previous PR

061589b

update megafusion output to _fusion_data.vcf

b4e2461

prettify

91f65d0

update modules from nf-core, update picard collectrnametrics container

c715953

update changelog with picard update

5ee433c

Merge pull request #395 from nf-core/update_filenames

6282473

Update filenames

update version number and changelog release formatting

fcde1cc

Merge pull request #399 from nf-core/release_2.4.0

8f49214

update version number and changelog release formatting

rannick requested review from maxulysse and apeltzer September 13, 2023 15:03

rannick self-assigned this Sep 13, 2023

maxulysse reviewed Sep 14, 2023

View reviewed changes

tower.yml Outdated Show resolved Hide resolved

rannick and others added 8 commits September 15, 2023 15:19

add descriptions of report files in tower.yml and correct output docu…

16b702e

…mentation

Update docs/output.md

b6d7498

Co-authored-by: Vadym <[email protected]>

fix formatting

0b74b7f

fix formatting

aafd2d0

Merge pull request #401 from nf-core/tower_info

6dfedc2

add descriptions of report files in tower.yml and correct output docu…

Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases

f876680

Merge pull request #403 from nf-core/update_fusionreport

14a69c2

Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases

update changelog

62f78be

rannick requested a review from maxulysse September 18, 2023 15:15

rannick added 2 commits September 20, 2023 10:22

change release date, uncomment institutional config again (issue with…

f3a09cd

… merging)

correct entry in changelog attributed to wrong release

3d24c12

maxulysse approved these changes Sep 22, 2023

View reviewed changes

rannick merged commit c3b0f9f into master Sep 25, 2023
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Release 2.4.0 #400

Release 2.4.0 #400

rannick commented Sep 13, 2023

github-actions bot commented Sep 13, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

maxulysse commented Sep 18, 2023

apeltzer commented Sep 19, 2023

Release 2.4.0 #400

Release 2.4.0 #400

Conversation

rannick commented Sep 13, 2023

PR checklist

github-actions bot commented Sep 13, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

maxulysse commented Sep 18, 2023

apeltzer commented Sep 19, 2023

github-actions bot commented Sep 13, 2023 •

edited

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