Template update #8

muffato · 2023-07-12T07:29:34Z

Closes #2.

Here I've updated the pipeline template from 2.5 to 2.8, one version at a time.

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).

github-actions · 2023-07-12T07:29:56Z

Python linting (`black`) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

Install black: pip install black
Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

github-actions · 2023-07-12T07:31:11Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit d865d02

+| ✅ 131 tests passed       |+
#| ❔  22 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-sequencecomposition_logo_light.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: docs/images/nf-core-sequencecomposition_logo_light.png
files_exist - File is ignored: docs/images/nf-core-sequencecomposition_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
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 ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-sequencecomposition_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sequencecomposition/sequencecomposition/.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/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: lib/WorkflowSequencecomposition.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-sequencecomposition_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 manifest.version ends in dev: '1.1dev'
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
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (74 files)
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: 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: ci.yml
actions_schema_validation - Workflow validation passed: branch.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: linting_comment.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 2023-08-11 07:08:26

muffato · 2023-07-12T11:30:59Z

The CI fails when doing the "full" test because there isn't enough space on disk 😁 The regular test does work already.

I'll try to reduce the disk usage, probably by trimming the samplesheet.

…ine sub-directories

muffato · 2023-08-04T12:49:14Z

Added a few commits to address issues actually found in sanger-tol/ensemblgenedownload#6 and a commit to enable the cleanup profile for our Tower tests and close #9

priyanka-surana

Almost there, a few changes to documentation.

.github/workflows/sangerfulltest.yml

.github/workflows/sangertest.yml

.nf-core.yml

CHANGELOG.md

priyanka-surana

LGTM 👍🏼 Thanks for making the changes

muffato added 2 commits September 12, 2022 08:30

initial template build from nf-core/tools, version 2.5

972cd85

Template update for nf-core/tools version 2.6

c998e1a

muffato linked an issue Jul 12, 2023 that may be closed by this pull request

Update pipeline template #2

Open

muffato added 14 commits July 12, 2023 09:05

Merge branch 'TEMPLATE' into dev

a6af3d3

Corrected the pipeline name

4029d4b

Manual fixes

56f497f

Template update for nf-core/tools version 2.7

d732cf0

Template update for nf-core/tools version 2.8

56f3fed

Merge branch 'TEMPLATE' into dev

ca10727

Merge branch 'TEMPLATE' into dev

a82485a

nf-core lint

7951f68

Fixed the path of the modules

329795e

New logo

2253a5f

I don't want to enforce cleanup=true here

ea829de

[linting] Applied black

9e64c21

[linting] Applied prettier

ee55f5d

Merge branch 'TEMPLATE' into dev

f8ae514

muffato force-pushed the template_update branch from eb1d434 to f8ae514 Compare July 12, 2023 10:25

Exclude .cff files from EditorConfig

16dce3d

muffato requested a review from priyanka-surana July 12, 2023 11:29

muffato marked this pull request as ready for review July 12, 2023 11:29

muffato added the maintain Tasks to keep pipelines up to date label Jul 15, 2023

muffato added 2 commits July 15, 2023 22:09

Fixed the example params.yaml

e4dd15f

Put these back at their original location

e51bebb

muffato added enhancement Improvement of the existing features and removed enhancement Improvement of the existing features labels Jul 16, 2023

The template was erroneously hardcoding sanger-tol/readmapping

55690e8

muffato added 6 commits July 31, 2023 21:45

Added a redirection notice to the pipeline website

0aadad0

The convention is now to put all the pipeline_info files in per-pipel…

5cc91c7

…ine sub-directories

Updated the DOI

dcf1c1f

Fixed the README

2f17c83

Should default to "results" for consistency

657ebcc

Added the farm tests (through Tower)

27404b2

muffato added 3 commits August 4, 2023 13:33

Reduced samplesheet that should take less space

9d6d4ea

Only download specific assemblies

6166bfa

Added back GITHUB_WORKSPACE

45f3ff4

priyanka-surana suggested changes Aug 9, 2023

View reviewed changes

.github/workflows/sangerfulltest.yml Outdated Show resolved Hide resolved

.github/workflows/sangertest.yml Outdated Show resolved Hide resolved

.nf-core.yml Show resolved Hide resolved

CHANGELOG.md Show resolved Hide resolved

muffato added 3 commits August 10, 2023 16:55

Latest nomenclature

19d9743

Added the code of conduct

411fa82

Fixed the CHANGELOG

d865d02

muffato requested a review from priyanka-surana August 11, 2023 07:20

priyanka-surana approved these changes Aug 11, 2023

View reviewed changes

muffato merged commit 6f15ef7 into dev Aug 11, 2023

muffato deleted the template_update branch August 11, 2023 10:07

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Template update #8

Template update #8

muffato commented Jul 12, 2023 •

edited

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github-actions bot commented Jul 12, 2023

github-actions bot commented Jul 12, 2023 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

muffato commented Jul 12, 2023

muffato commented Aug 4, 2023

priyanka-surana left a comment

priyanka-surana left a comment

Template update #8

Template update #8

Conversation

muffato commented Jul 12, 2023 • edited Loading

PR checklist

github-actions bot commented Jul 12, 2023

Python linting (black) is failing

github-actions bot commented Jul 12, 2023 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

muffato commented Jul 12, 2023

muffato commented Aug 4, 2023

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muffato commented Jul 12, 2023 •

edited

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Python linting (`black`) is failing

github-actions bot commented Jul 12, 2023 •

edited

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`nf-core lint` overall result: Passed ✅