Template update #10

muffato · 2023-07-15T09:05:49Z

Closes #7
I've updated the pipeline template from 2.5 to 2.8.

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 · 2023-07-15T09:11:42Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit e24a6f7

+| ✅ 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-insdcdownload_logo_light.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: docs/images/nf-core-insdcdownload_logo_light.png
files_exist - File is ignored: docs/images/nf-core-insdcdownload_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-insdcdownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-insdcdownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-insdcdownload_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/insdcdownload/insdcdownload/.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/WorkflowInsdcdownload.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-insdcdownload_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: '1.2dev'
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 (80 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 07:08:29

priyanka-surana

Some minor comments but mostly good to go. Testing ran successfully. Might be worth looking at the output structure when assembly is not in ToL.

.nf-core.yml

README.md

assets/slackreport.json

docs/usage.md

nextflow.config

Co-authored-by: Priyanka Surana <[email protected]>

github-actions · 2023-07-31T11:03:53Z

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!

…ine sub-directories

…website

muffato · 2023-08-01T07:35:21Z

Might be worth looking at the output structure when assembly is not in ToL.

Thank you for the nudge, and I think I know what to change. I can give an overview at the daily today and I'll create a ticket for the next sprint.

muffato · 2023-08-04T09:32:43Z

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 #11

muffato added 10 commits July 14, 2023 09:56

Template update for nf-core/tools version 2.6

0a9c648

Template update for nf-core/tools version 2.7

9e07b9b

Template update for nf-core/tools version 2.8

93863d6

[linting] prettier

bfce31f

[linting] black

31e5f8c

Merge branch 'TEMPLATE' into dev

ed0b297

Merge branch 'TEMPLATE' into dev

9284bfb

Merge branch 'TEMPLATE' into dev

bcb2b50

Fixed the modules installation

23f24b7

Fixed the modules path

9268ef6

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

muffato linked an issue Jul 15, 2023 that may be closed by this pull request

Update pipeline template #7

Open

muffato added 2 commits July 15, 2023 10:09

Now need nf-core 2.8

2d86b29

we use prettier for the cff files

f9dadd0

muffato added 8 commits July 15, 2023 10:24

Need to use Nextflow.error

cb4d091

[linting] prettier

4540aa1

Fixed the Conda directives

931c243

The quay.io prefix should now be skipped

435fcf1

No output for Tower

a9551d5

We don't use MultiQC

1d2524a

Fixed the wget conda package

7254f04

[linting] prettier

890dbb6

muffato marked this pull request as ready for review July 15, 2023 13:26

muffato added 6 commits July 15, 2023 21:56

was 2 before the template update

e903d25

We do this through a profile

81178e5

Fixed the example params.yaml

b540ef3

[linting] prettier

9682670

We don't make shared sanger-tol workflows anymore

d7951cf

Not needed

f17c776

This file is now identical

d3ade99

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

muffato requested a review from priyanka-surana July 17, 2023 08:43

priyanka-surana approved these changes Jul 31, 2023

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.nf-core.yml Outdated Show resolved Hide resolved

README.md Outdated Show resolved Hide resolved

assets/slackreport.json Outdated Show resolved Hide resolved

docs/usage.md Outdated Show resolved Hide resolved

nextflow.config Outdated Show resolved Hide resolved

Leftover from a copy

8d9bc1c

Co-authored-by: Priyanka Surana <[email protected]>

muffato added 5 commits July 31, 2023 11:04

Added a redirection notice to the pipeline website

7b33db6

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

c2a374f

…ine sub-directories

Added the code of conduct back

7777314

There is no parameters.md page anymore

00badc4

Fixed README - now matching the template and linking to the pipeline …

3c42dfa

…website

muffato added 4 commits August 4, 2023 09:29

Updated the DOI

44fbe8b

This is superfluous

24eea75

Updated the contributions

a94039d

Added options to submit the pipelines to the farm from GitHub

322ca6c

muffato force-pushed the template_update branch from 86da62c to 322ca6c Compare August 4, 2023 09:29

muffato linked an issue Aug 4, 2023 that may be closed by this pull request

Add CI tests on the farm #11

Closed

muffato added 2 commits August 4, 2023 11:29

docfix

e1b927d

Latest nomenclature

e24a6f7

muffato merged commit aa2a366 into dev Aug 11, 2023

muffato deleted the template_update branch August 11, 2023 09:43

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Template update #10

Template update #10

muffato commented Jul 15, 2023

github-actions bot commented Jul 15, 2023 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

priyanka-surana left a comment

github-actions bot commented Jul 31, 2023

muffato commented Aug 1, 2023

muffato commented Aug 4, 2023

Template update #10

Template update #10

Conversation

muffato commented Jul 15, 2023

PR checklist

github-actions bot commented Jul 15, 2023 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

priyanka-surana left a comment

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github-actions bot commented Jul 31, 2023

Python linting (black) is failing

muffato commented Aug 1, 2023

muffato commented Aug 4, 2023

github-actions bot commented Jul 15, 2023 •

edited

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`nf-core lint` overall result: Passed ✅

Python linting (`black`) is failing