Release 2.0 #11

muffato · 2024-05-23T17:19:56Z

Like in sanger-tol/insdcdownload#16, this PR is to finally release all the code that's been sitting on the dev branch for a while. All the individual changes have been reviewed in previous pull-requests and the only extra commits I've added are to update the changelog and the version numbers

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).

Except the iterators that were groovy maps

Support new FTP structure + output directory

…e longest sequence

…d in the GFF file

Template update

Use the latest version of the Tower action

New tolsoft details

Rework of the output directories

github-actions · 2024-05-23T17:21:25Z

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

Posted for pipeline commit 637edc8

+| ✅ 129 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0.0'

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-ensemblgenedownload_logo_light.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_logo_light.png
files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_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/branch.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-ensemblgenedownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ensemblgenedownload/ensemblgenedownload/.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/WorkflowEnsemblgenedownload.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-ensemblgenedownload_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/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 (78 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.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: 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 2024-06-04 08:51:13

gq1 · 2024-06-03T14:03:22Z

#12

Ci branch check to main not master

muffato · 2024-06-03T17:39:31Z

Done

muffato added 30 commits September 25, 2022 13:50

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

1fa040d

Version bump on dev

0e85b5c

Added support for the annotation method

f7546d1

typo

32ecbd9

Documentation update

8f65859

Added a check

cec6ce9

Evaluate relative paths from --outdir

8bb1ce7

Linting: prettier, black, and updated nf-core yaml

80ebc48

Pinning the version of nf-core as long as this is a 2.5 pipeline

112a1af

--outdir should actually be considered a mandatory parameter

c59c4f7

Converted most "it" iterators to explicitly-named variables

f7f1719

Except the iterators that were groovy maps

Removed extra }

16a2312

Merge pull request #2 from sanger-tol/new_ftp

af6a773

Support new FTP structure + output directory

Updated logo

7bceea5

Typo: assembly_name is not a recognised command-line parameter

de69ba1

Added 130 for MEMLIMIT

45f24e4

Don't complain about missing files on the Ensembl FTP

3cdab16

Read properties of the fasta file, and augment meta

f8abd23

samtools dict needs an amount of RAM proportional to the length of th…

95fa096

…e longest sequence

Select the right tabix indexing based on the coordinates actually use…

9003772

…d in the GFF file

Updated tag to match the convention

a47cad2

For comprehensiveness, provide channels for the unavailable indices

def4ff6

Adjusted the memory requirement for sort+tabix

bad66d0

Updated the change-log

e06d280

Doc update

8653486

Nextflow version bump due to the way Conda is enabled/disabled

e50ca13

Documentation update

d6f0bba

Documentation update

86d4aeb

Brought some consistency

6176673

Merge branch 'full_test' into dev

cb668f6

muffato and others added 16 commits August 4, 2023 11:21

Added the farm tests (through Tower)

0acf02a

prettier

f56341b

Latest nomenclature

ba5dcba

The warning should be on the README too

02a0b32

Merge pull request #6 from sanger-tol/template_update

2cf5ba2

Template update

Now use "outdir", which is equivalent to a ToL analysis directory

693c53d

Use the latest version of the Tower action

d041a70

Update sanger_test.yml

30f351c

Update sanger_test_full.yml

085ee2a

Update sanger_test_full.yml

cab4333

Merge pull request #9 from sanger-tol/tower_action

96c499c

Use the latest version of the Tower action

New tolsoft details

147d668

Fixed the repository name

24e75ee

Merge pull request #10 from sanger-tol/new_tolsoft_details

63d5bdc

New tolsoft details

Made the relation between --outdir and the samplesheet outdir clearer

27b5e8a

Merge pull request #8 from sanger-tol/outdir

04b7a5e

Rework of the output directories

muffato self-assigned this May 24, 2024

muffato added 2 commits May 24, 2024 18:33

Version bump

49e2311

Updated the changelog

8ebe0ce

muffato added bug Something isn't working enhancement Improvement of the existing features labels May 28, 2024

gq1 added 2 commits June 3, 2024 15:00

change default branch to main for PR branch checking

d095e4b

Add one more unchanged file for nf-core linting

bcc3f29

Merge pull request #12 from sanger-tol/ci_branch

697f1be

Ci branch check to main not master

gq1 approved these changes Jun 3, 2024

View reviewed changes

Updated the release date

637edc8

muffato merged commit 5a8e597 into main Jun 4, 2024
13 checks passed

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Release 2.0 #11

Release 2.0 #11

muffato commented May 23, 2024 •

edited

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github-actions bot commented May 23, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Jun 3, 2024

muffato commented Jun 3, 2024

Release 2.0 #11

Release 2.0 #11

Conversation

muffato commented May 23, 2024 • edited Loading

PR checklist

github-actions bot commented May 23, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Jun 3, 2024

muffato commented Jun 3, 2024

muffato commented May 23, 2024 •

edited

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github-actions bot commented May 23, 2024 •

edited

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