1.3.0 release #395

DLBPointon · 2025-04-09T09:22:20Z

aaand again....

Update naming of module in config

github-actions · 2025-04-09T09:24:37Z

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

Posted for pipeline commit 48587f8

+| ✅ 126 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.3.0'
pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
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 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/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ 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: conf/modules.config
files_exist - File found: conf/test.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/WorkflowTreeval.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-treeval_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/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 - 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
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: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (451 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/yaml'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 2025-04-15 15:34:51

DLBPointon · 2025-04-09T09:52:12Z

502 gateway error, rerunning failed jobs

Update base.config

DLBPointon · 2025-04-09T15:55:19Z

@yumisims We need you to approve this one please

DLBPointon · 2025-04-10T08:34:24Z

Actually, can we pause this whilst I get the CHANGELOG updated and push in this fix for telo.

This is now here: #398

… starting with '>'

Update CHANGELOG

Softmasked telo fix

fixed threshold

Fine telomere nostrongwords

change bamtobed_sort memory

Pretextgraph resource + bam2bed_sort memory fix

Final changes for 1.3.0

DLBPointon and others added 2 commits April 8, 2025 16:10

Update naming of module in config

c141a59

Merge pull request #394 from sanger-tol/config_change

7bbe627

Update naming of module in config

DLBPointon requested review from yumisims and weaglesBio April 9, 2025 09:22

DLBPointon self-assigned this Apr 9, 2025

weaglesBio approved these changes Apr 9, 2025

View reviewed changes

DLBPointon and others added 2 commits April 9, 2025 11:50

Update base.config

8e5639a

Merge pull request #396 from sanger-tol/mem_patch1

b875f8b

Update base.config

DLBPointon and others added 17 commits April 10, 2025 09:54

subworkflows/local

aebc1c9

adding gawk

840e617

Update CHANGELOG

2b3d317

Fix module path

13b0c29

Current min version of nextflow does not support arity

fde2b38

update post patch

e1e10bd

Adding UPPERCASE function to remove errant lowercase letters in lines…

03000ba

… starting with '>'

Re-organise the GAWK order

c2e243b

Escape the GAWK

92717b8

Escape the GAWK

dbbb2b8

Spelling mistake

6529241

Update CHANGELOG.md

4c89db7

Update CHANGELOG

Merge pull request #398 from sanger-tol/softmasked_telo_fix

00c5bd6

Softmasked telo fix

fixed threshold

b24702f

Merge pull request #400 from sanger-tol/telomereconscore

fcbb244

fixed threshold

no strong words

0985bd0

Merge pull request #401 from sanger-tol/fine_telomere_nostrongwords

8d24af3

Fine telomere nostrongwords

DLBPointon requested a review from weaglesBio April 14, 2025 13:51

yumisims and others added 4 commits April 14, 2025 16:57

Update pretext_graph.nf

5ee86eb

Update base.config

eddb03e

change bamtobed_sort memory

Merge branch 'dev' into pretextgraph_resource

c31292f

Merge pull request #403 from sanger-tol/pretextgraph_resource

ba411eb

Pretextgraph resource + bam2bed_sort memory fix

DLBPointon changed the title ~~1.2.3 release~~ 1.3.0 release Apr 15, 2025

DLBPointon and others added 4 commits April 15, 2025 14:48

CHANGELOG update

8671d6f

CHANGELOG and version update

c0d1f47

CHANGELOG LINT

b38b127

Merge pull request #404 from sanger-tol/final_changed

48587f8

Final changes for 1.3.0

yumisims approved these changes Apr 15, 2025

View reviewed changes

DLBPointon merged commit 7162e7f into main Apr 16, 2025
14 checks passed

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1.3.0 release #395

1.3.0 release #395

DLBPointon commented Apr 9, 2025

github-actions bot commented Apr 9, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Apr 9, 2025

DLBPointon commented Apr 9, 2025

DLBPointon commented Apr 10, 2025 •

edited

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1.3.0 release #395

1.3.0 release #395

Conversation

DLBPointon commented Apr 9, 2025

github-actions bot commented Apr 9, 2025 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Apr 9, 2025

DLBPointon commented Apr 9, 2025

DLBPointon commented Apr 10, 2025 • edited Loading

github-actions bot commented Apr 9, 2025 •

edited

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

DLBPointon commented Apr 10, 2025 •

edited

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