Main to dev merge #345

DLBPointon · 2024-12-10T10:24:59Z

More back merging!

Dp24 jbrowse only

Steps into DEV not into MAIN

Dp24 module update 2

Add .ktab to output.

Dp24 module update samtools

Resources review

Dev

…r-tol/treeval into tola406_genesetsyntenyyaml

Simplify geneset and synteny params in .yaml by using full paths.

…a406_genesetsyntenyyaml

Will's Update to MerquryFK

github-actions · 2024-12-10T10:26:40Z

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

Posted for pipeline commit c10a9ab

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.2.0'
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/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/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 - 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 (436 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: 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: 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 2024-12-10 12:28:25

DLBPointon · 2024-12-10T12:35:41Z

There's too much thats been changed or deleted

DLBPointon and others added 30 commits November 15, 2024 11:46

Merge branch 'main' into dev

43b4cf0

Merge pull request #307 from sanger-tol/dp24_jbrowse_only

f7d9db2

Dp24 jbrowse only

Updates for modules, README and config

cb5d998

Add ktab to output

8aad21a

Update documentation

ca2afc4

Merge pull request #330 from sanger-tol/dp24_steps

52f5bf9

Steps into DEV not into MAIN

Updating SAMTOOLS

79bd32f

linting

217bd32

Updating all easy to update modules

30a576c

Updating all easy to update modules

e93fd9a

Updating all easy to update modules

dc1e076

Updating all easy to update modules

3c660bb

Fixes to modules

32152a5

linting

1beeeb5

Patches

ae7380c

Merge branch 'dev' of https://github.com/sanger-tol/treeval into dev

27439f5

Adding steps to skip BUSCO

4ad0c65

Pinning BUSCO to V5.5

160af01

Removing steps var

55ed6d6

Linting

0ada598

Merge pull request #335 from sanger-tol/dp24_module_update_2

85217d9

Dp24 module update 2

Merge pull request #327 from sanger-tol/tola399_outputktab

701b19b

Add .ktab to output.

Minor updates

9268b77

Resources review

8356733

Merge pull request #333 from sanger-tol/dp24_module_update_samtools

7a0ca25

Dp24 module update samtools

Merge pull request #336 from sanger-tol/tola401_updateresources

b9600d9

Resources review

add binfile output and update pretext_graph

0ecff8d

add binfile output and update pretext_graph

26a41a8

Updating last of NF-core modules

cc96248

Merge pull request #338 from sanger-tol/dev

107582a

Dev

DLBPointon and others added 22 commits November 29, 2024 16:02

Updates to Synteny to reflect Minimap2 update

163ffd6

Update yahs

9b78df1

Change to YAML_INPUT

b084e7c

lint fix

e7e36d1

Change SETUP from 1 to 2.14

c1e52e8

Change SETUP from 1 to 2.14

10212a8

Bump BAM2BED SORT to 2Gb as base

781615e

Adding VERSION information!

a929f2f

Making sure version information is printed

96f47fd

removing defaults

68a38a8

Update TreeValTinyFullTest.yaml

d87bed7

Update TreeValTinyFullTest.yaml

49f9ea5

Merge branch 'tola406_genesetsyntenyyaml' of https://github.com/sange…

4f211f7

…r-tol/treeval into tola406_genesetsyntenyyaml

Updates for field value and PRETTER!

18688d6

Updates

233b326

Merge pull request #340 from sanger-tol/tola406_genesetsyntenyyaml

436cd12

Simplify geneset and synteny params in .yaml by using full paths.

Merge remote-tracking branch 'origin/tola413_merquryfkfault' into tol…

e018c0d

…a406_genesetsyntenyyaml

Wills MerquryFK update

0bdcf5d

Revert modules.json to previous PR

c55ea9b

Merge pull request #344 from sanger-tol/tola406_genesetsyntenyyaml

007cb12

Will's Update to MerquryFK

Merge branch 'dev' of https://github.com/sanger-tol/treeval into dev

f5c6ef1

merge conflict fix... hopefully

7821b6c

DLBPointon requested a review from weaglesBio December 10, 2024 10:24

DLBPointon self-assigned this Dec 10, 2024

DLBPointon added 3 commits December 10, 2024 12:16

Left in some merge headers

f4c9881

Merge conflict and config addition

f281eb1

Why did the container revert?

c10a9ab

DLBPointon closed this Dec 10, 2024

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Main to dev merge #345

Main to dev merge #345

DLBPointon commented Dec 10, 2024

github-actions bot commented Dec 10, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Dec 10, 2024

Main to dev merge #345

Main to dev merge #345

Conversation

DLBPointon commented Dec 10, 2024

github-actions bot commented Dec 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Dec 10, 2024

github-actions bot commented Dec 10, 2024 •

edited

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