Dp24 steps #319

DLBPointon · 2024-09-05T16:06:17Z

Adding --steps param, each workflow is now togglable.

I'm not sure why the lib keeps getting deleted and re-added and in the wrong place.

Main to Dev

…not very NF-Core

…308

github-actions · 2024-09-05T16:09:48Z

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

Posted for pipeline commit 35d9f23

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

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.1.1'
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 (344 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.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 2024-11-15 15:23:18

DLBPointon · 2024-09-17T13:24:14Z

Revert the moving of Lib.

DLBPointon · 2024-11-15T12:37:50Z

There were a further 2 modules using the no longer available quay.io/sanger-tol/cram-filter... container.

Now corrected.

weaglesBio

Looks good

Update cram_filter_minimap2_filter5end_fixmate_sort.nf

Update main.nf

DLBPointon and others added 15 commits June 27, 2024 15:53

Adding new line

5882074

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

4ebc614

New workflow on request from GRIT, closes #305

42b846e

Add support for new workflow

b3bd2cd

Testing arch to fix pretext

4210ca0

Add support for new workflow

d3a98e3

Merge pull request #306 from sanger-tol/main

3f88a62

Main to Dev

Correction

b82e921

Correction

e81653d

Added version output and removed the liberal use of spaces which are …

4af6d93

…not very NF-Core

Remove dp24's liberal use of spaces - not very nf-core

8c4b7b9

added conda not available quotes to modules lacking conda envs closes #…

5964920

…308

Fixes to modules

70a771a

Fix variable

24bfc60

Additions of steps flag

e4b4cf0

DLBPointon requested review from yumisims and weaglesBio September 17, 2024 13:12

DLBPointon added 2 commits September 19, 2024 17:05

removing lib from docs

7c72815

Updated Docs

205dadc

DLBPointon mentioned this pull request Nov 14, 2024

Flags to run X subworkflow #115

Closed

DLBPointon added 8 commits November 15, 2024 11:00

Merge branch 'dev' into dp24_steps

da9cb5e

Linting

2de9d8e

Merge branch 'dev' into dp24_jbrowse_only

fc86857

Merged from main

9fbbc11

Updating container

032aab6

Updating container

4b0fc99

Update to add default to flag

9d10300

Update to add default to flag

10f0508

DLBPointon added 2 commits November 15, 2024 12:16

Update to add default to flag

382f7f4

Update to add default to flag

5fb3c96

DLBPointon linked an issue Nov 15, 2024 that may be closed by this pull request

Add steps for subworkflows #317

Closed

DLBPointon added 2 commits November 15, 2024 12:35

Update to add default to flag

8407bfc

Another incorrect container

dd8ac09

weaglesBio approved these changes Nov 15, 2024

View reviewed changes

DLBPointon and others added 5 commits November 15, 2024 15:16

Update main.nf

e6be044

Update cram_filter_minimap2_filter5end_fixmate_sort.nf

9e375d5

Merge pull request #325 from sanger-tol/DLBPointon-patch-2

6358ab3

Update cram_filter_minimap2_filter5end_fixmate_sort.nf

Merge pull request #326 from sanger-tol/DLBPointon-patch-1

919a7f6

Update main.nf

Merge with dp24_jbrowse_only

35d9f23

DLBPointon requested a review from weaglesBio November 15, 2024 16:08

weaglesBio approved these changes Nov 15, 2024

View reviewed changes

DLBPointon merged commit 4c9f8cd into main Nov 15, 2024
6 checks passed

DLBPointon deleted the dp24_steps branch November 15, 2024 16:28

DLBPointon restored the dp24_steps branch November 19, 2024 14:52

DLBPointon mentioned this pull request Nov 19, 2024

Revert "Dp24 steps" #328

Merged

DLBPointon deleted the dp24_steps branch November 20, 2024 10:57

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Dp24 steps #319

Dp24 steps #319

DLBPointon commented Sep 5, 2024 •

edited

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github-actions bot commented Sep 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Sep 17, 2024

DLBPointon commented Nov 15, 2024

weaglesBio left a comment

Dp24 steps #319

Dp24 steps #319

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DLBPointon commented Sep 5, 2024 • edited Loading

github-actions bot commented Sep 5, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Sep 17, 2024

DLBPointon commented Nov 15, 2024

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DLBPointon commented Sep 5, 2024 •

edited

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github-actions bot commented Sep 5, 2024 •

edited

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