2.1.0 release #161

tkchafin · 2024-12-13T17:48:02Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

…AGAT_SQSTATBASIC'

Added new subworkflow 'ANNOTATION_STATS' and new parameter --annotation_set to solve issue #121

…s information from the txt files

…sic processes

Anaconda purge

nf-core samtools/view updated

Anaconda purge (2.x.x)

Release 2.1.0

Update CHANGELOG.md

removed merquryfk

github-actions · 2024-12-13T17:49:20Z

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

Posted for pipeline commit ee78df8

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.1.0'

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
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/workflows/linting.yml
files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
template_strings - template_strings

✅ 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/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/modules.config
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: 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: lib/WorkflowGenomenote.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-genomenote_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.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: 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.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 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 - .github/.dockstore.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 - 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
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
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_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-12-16 09:38:07

Fixed the CI by switching to the v2 of the action

muffato · 2024-12-16T14:20:44Z

(multiqc seems flaky on the CI, but I think it's still OK to release)

SandraBabirye and others added 30 commits August 15, 2024 20:06

added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'

7dc9838

added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'

0548d90

added new subworkflow to obtain annotation summary statistics

cfafbaa

added params.annotation_set

ddc3edc

added documentation for params.annotation_set

3bd733a

added annotation_stats as specific output directory

131b7b8

allocated resources for the two new processes 'AGAT-SPSTATISTICS and …

e98a375

…AGAT_SQSTATBASIC'

added new subworkflow and params.annotation_set

5a2abe7

added path to the test annotation file

c35db05

modified the file after running prettier

2fc43e8

added a new subworkflow 'ANNOTATION_STATS)

a8dbd78

Edited annotation_statistics.nf file

da91c57

edited the pattern for --annotation_set to include gff rather than gff3

65b463e

edited the pattern for --annotation_set to include gff rather than gff3

85ac505

Merge pull request #135 from sanger-tol/annotation_statistics

7e201c7

Added new subworkflow 'ANNOTATION_STATS' and new parameter --annotation_set to solve issue #121

added a python script that extracts the relevant annotation statistic…

26bd58c

…s information from the txt files

added a new local module to extract annotation statistics information

fe3c78e

edited the annotation_stats subworkflow to include the new local module

fd0d992

adjusted the allocated memory for agat_spstatistics and agat_sqstatba…

e6c6778

…sic processes

edited the annotation_stats subworkflow to include the new local module

ead4298

edited the annotation_stats subworkflow to include the new local module

a52bc5d

edited the annotation_stats subworkflow and removed .out

054dade

edited the modules.confif file

0e316cd

edited the file

5902545

edited the file

0f8b9ae

edited file

5b6db7a

edited file

fe44659

edited file

d715b26

edited file

9b21ccf

edited file

5735681

tkchafin and others added 24 commits November 22, 2024 15:41

update nf-core/bamtobed

6cc12cd

nf-core/busco updated to 5.7.1 and patched

13687d9

nf-core/cooler updated

798369b

nf-core/dumpsoftwareversions updated

c9e4211

nf-core/gffread updated

061ac2e

nf-core module updates

1f18dad

nf-core module updates

bd8bfaa

remove anaconda references

dd58ec1

Merge pull request #153 from tkchafin/anaconda_purge

4a86006

Anaconda purge

nf-core samtools/view updated

f6220c0

Merge pull request #154 from tkchafin/anaconda_purge

2930baf

nf-core samtools/view updated

remote deprecated cleanup=true

a01d592

Update CHANGELOG.md

2f5b69b

Update CHANGELOG.md

c4e97c3

Merge pull request #155 from sanger-tol/anaconda_purge

5f89876

Anaconda purge (2.x.x)

Merge branch 'dev' into Release-2.1.0

4eb4aa6

prettier fix

bbfada7

Update Utils.groovy

e448f75

Merge pull request #152 from sanger-tol/Release-2.1.0

e11e4a8

Release 2.1.0

Update CHANGELOG.md

bf9e345

Merge pull request #158 from sanger-tol/changelog

8b9de0f

Update CHANGELOG.md

removed merquryfk

44f238e

prettier linting

8add69e

Merge pull request #160 from tkchafin/merquryfk

1092fdc

removed merquryfk

tkchafin requested a review from muffato December 13, 2024 17:48

muffato and others added 2 commits December 13, 2024 22:33

Fixed the CI by switching to the v2 of the action

974f5cc

Merge pull request #162 from sanger-tol/ci

ee78df8

Fixed the CI by switching to the v2 of the action

muffato approved these changes Dec 16, 2024

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2.1.0 release #161

2.1.0 release #161

tkchafin commented Dec 13, 2024

github-actions bot commented Dec 13, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

muffato commented Dec 16, 2024

2.1.0 release #161

Are you sure you want to change the base?

2.1.0 release #161

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tkchafin commented Dec 13, 2024

PR checklist

github-actions bot commented Dec 13, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

muffato commented Dec 16, 2024

github-actions bot commented Dec 13, 2024 •

edited

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