Release 2.0 #11

muffato · 2024-05-23T17:19:45Z

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

…w meta keys

Template update

Use the latest version of the Tower action

New tolsoft details

Rework of the output directories

github-actions · 2024-05-23T17:21:12Z

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

Posted for pipeline commit b0f7829

+| ✅ 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-ensemblrepeatdownload_logo_light.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: docs/images/nf-core-ensemblrepeatdownload_logo_light.png
files_exist - File is ignored: docs/images/nf-core-ensemblrepeatdownload_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-ensemblrepeatdownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-ensemblrepeatdownload_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-ensemblrepeatdownload_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ensemblrepeatdownload/ensemblrepeatdownload/.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/WorkflowEnsemblrepeatdownload.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-ensemblrepeatdownload_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 (79 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 08:44:14

gq1 · 2024-06-03T13:52:58Z

#12

Ci branch check to main not master

muffato · 2024-06-03T18:27:22Z

Done

muffato added 30 commits October 19, 2022 01:50

Version bump on dev

b16c113

Added support for the annotation method

d64deb4

Evaluate relative paths from --outdir

bb741a4

We currently expect the extra sanger-tol lines in this file

f0de6e0

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

d74ec90

--outdir should actually be considered a mandatory parameter

4429a4b

Removed extra }

9609f43

Converted most "it" iterators to explicitly-named variables

5fb68bf

Except the iterators that were groovy maps

Merge pull request #2 from sanger-tol/new_ftp

c640f94

Support new FTP structure + output directory

Updated logo

e652647

Typo: assembly_name is not a recognised command-line parameter

e40fd54

Added 130 for MEMLIMIT

76316f4

Don't complain about missing files on the Ensembl FTP

91e59ad

Read properties of the fasta file, and augment meta

46ef3e6

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

3328f85

…e longest sequence

Make prepare_repeats select the right tabix indexing thanks to the ne…

eec9154

…w meta keys

For comprehensiveness, provide channels for the unavailable indices

ee4eb38

My convention is to have two blank lines there

9050bae

Doc update

4fdbaa3

Updated the change-log

091bc85

Optimised resource usage for tabix too

e9441a5

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

61ceda6

Documentation update

a1a6200

Documentation update

28af129

Brought some consistency

c9224e1

Merge branch 'full_test' into dev

08a0350

Fixed the pipeline name

19b9f68

Template update for nf-core/tools version 2.6

c8e3b80

Merge branch 'TEMPLATE' into dev

7384fb8

Template update for nf-core/tools version 2.7

5321874

muffato and others added 14 commits August 11, 2023 02:35

The warning should be on the README too

ff47946

Latest nomenclature

b177af0

Merge pull request #6 from sanger-tol/template_update

919c1f4

Template update

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

d649e81

Use the latest version of the Tower action

ec56e9b

Update sanger_test.yml

6b9a55d

Update sanger_test_full.yml

0a98259

Update sanger_test_full.yml

fbdb59f

Merge pull request #9 from sanger-tol/tower_action

009c212

Use the latest version of the Tower action

New tolsoft details

fd35531

Fixed the repository name

e6c2599

Merge pull request #10 from sanger-tol/new_tolsoft_details

c1ef111

New tolsoft details

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

ccd9211

Merge pull request #8 from sanger-tol/outdir

1b89a66

Rework of the output directories

muffato added 3 commits May 24, 2024 18:31

Version bump

eb9f6bf

Updated the output documentation

97516bd

Changelog updated

9b0138b

muffato self-assigned this May 24, 2024

muffato added enhancement Improvement of the existing features bug Something isn't working labels May 24, 2024

gq1 added 2 commits June 3, 2024 14:49

change default branch to main for PR branch checking

dd8c9ca

add one more unchanged file for nf-core linting

a6b54fa

Merge pull request #12 from sanger-tol/ci_branch

8373ab3

Ci branch check to main not master

gq1 approved these changes Jun 3, 2024

View reviewed changes

Updated the release date

b0f7829

muffato merged commit 21757b3 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 ✅ ⚠️