Dp24 spelling #45

DLBPointon · 2024-12-05T13:48:25Z

Module updates and container changes.

Version upped to V1.1

DLBPointon · 2024-12-05T13:49:02Z

Will hopefully solve issues with #42 and #43

github-actions · 2024-12-05T13:50:22Z

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

Posted for pipeline commit 3d75460

+| ✅ 122 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: '1.1.0'
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in base.config: Check the defaults for all processes
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
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
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/PULL_REQUEST_TEMPLATE.md
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/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
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/curationpretext/curationpretext/.github/workflows/awstest.yml
multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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: 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: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: lib/WorkflowCurationpretext.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-curationpretext_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/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html 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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (252 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
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
actions_schema_validation - Workflow validation passed: sanger_test.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-12-09 13:49:34

DLBPointon · 2024-12-06T09:43:00Z

Just remembered that CHANGELOG needs updating. I'll sort that out Monday!

muffato

I can confirm that:

all containers are Anaconda-free
no occurrence of defaults & co in the environment.yml files

You also need to update:

CITATIONS.md (there's a reference to Anaconda)
libs/Utils.groovy (to remove defaults from the channel list)

I've kicked off a test_full run and will check it on Monday, though I'm not sure I can fully assess the outputs make sense

muffato · 2024-12-06T17:54:20Z

test_full was actually quick ! The output files are identical 👍🏼

muffato · 2024-12-06T17:59:37Z

Ah wait, there are still occurrences of quay.io/sanger-tol/pretext:0.0.2-yy5-c3 (#42) !

modules/local/pretext_graph.nf:    container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"
modules/nf-core/pretextmap/main.nf:    container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"
modules/nf-core/pretextmap/pretextmap.diff:+    container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"

DLBPointon · 2024-12-09T09:59:41Z

Thanks for the review Matthieu, I've now just got to update Changelog. But currently debugging #43 and #44.

DLBPointon added 3 commits December 5, 2024 13:43

Updating

111aa60

Updating modules

080321e

Updating version to 1.1

84817a6

DLBPointon self-assigned this Dec 5, 2024

Merge branch 'dev' into dp24_spelling

28415b4

DLBPointon added 5 commits December 5, 2024 14:03

Updating more

4d72e53

prettier linting

d406a12

Updating setup from 1 to 2

058ed13

Adding tuple declaration

1e0f35e

Replace generate_csv singularity container

69fe17d

DLBPointon requested review from muffato and weaglesBio December 6, 2024 09:41

muffato reviewed Dec 6, 2024

View reviewed changes

DLBPointon added 4 commits December 9, 2024 09:47

Updating testing

8805be5

Replace 0.0.2-yy5-c3 with 0.0.3-yy5-c1

147b88f

Remove anaconda ref in Utils and CITATIONS

0eb48b6

PRETTIER

4a1b70f

DLBPointon added 2 commits December 9, 2024 10:23

Changing grep to actually get the version info

84b1bce

Removing params

ff74ae3

DLBPointon mentioned this pull request Dec 9, 2024

Perl version in wrong format #46

Closed

This was linked to issues Dec 9, 2024

Perl version in wrong format #46

Closed

Please update Pretext Docker image in nf-core modules #42

Closed

DLBPointon added 2 commits December 9, 2024 10:46

Changing version command, confirmed locally and in container

2764466

Changin PERL version string and Updating executor values

3c15e2d

DLBPointon added 4 commits December 9, 2024 12:40

Readding defaults

9ad902d

ONE SPACE caused version to not print

c6a2199

Correct versioning information in modules

55756f1

Updating the changelog

3d75460

DLBPointon requested a review from muffato December 9, 2024 15:10

muffato approved these changes Dec 9, 2024

View reviewed changes

DLBPointon merged commit 3100655 into dev Dec 10, 2024
6 checks passed

muffato deleted the dp24_spelling branch December 10, 2024 09:12

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Dp24 spelling #45

Dp24 spelling #45

DLBPointon commented Dec 5, 2024 •

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DLBPointon commented Dec 5, 2024

github-actions bot commented Dec 5, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Dec 6, 2024

muffato left a comment

muffato commented Dec 6, 2024

muffato commented Dec 6, 2024

DLBPointon commented Dec 9, 2024

Dp24 spelling #45

Dp24 spelling #45

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DLBPointon commented Dec 5, 2024 • edited Loading

DLBPointon commented Dec 5, 2024

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

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

DLBPointon commented Dec 6, 2024

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muffato commented Dec 6, 2024

muffato commented Dec 6, 2024

DLBPointon commented Dec 9, 2024

DLBPointon commented Dec 5, 2024 •

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github-actions bot commented Dec 5, 2024 •

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