Release 2.0.0 #146

BethYates · 2024-10-10T12:29:17Z

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).

…enome_note template file

…e to be wriiten to a results folder called genome_note

Genome metadata added module to produce a docx file from a genome note template file and genome metadata parameter file

…ess. requires a secret to be set defining a key for the portal API

…key to access genome notes database

Genome metadata

With 50MB I was having it fail and re-try

first directive is overwritten by second one, have tested that 2nd is correct! :)

One less container to fetch; have tested

…on_location parsing/matching better and include all linked assemblies

…into release_2.0_fixes

…dentifiers for the author string

Release 2.0 fixes

Release 2.0

github-actions · 2024-10-10T12:30:54Z

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

Posted for pipeline commit 5a54958

+| ✅ 131 tests passed       |+
#| ❔  21 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/nf-core-genomenote_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomenote_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
files_exist - File is ignored: conf/igenomes.config
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 does not exist: assets/nf-core-genomenote_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
template_strings - template_strings

✅ 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: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: lib/WorkflowGenomenote.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-genomenote_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/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 - assets/sendmail_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
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
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: 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
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-10-10 12:30:38

BethYates and others added 30 commits June 27, 2023 18:32

removed whitespace

f2bc386

requested changes from PR 70

3b00a13

give partially completed genome note template a meaningful name

3fe9461

renamed input to something more useful

997effd

Update linting.yml fix to nf-core 2.8.10

558fe76

added linting.yml to files_unchanged

45d7387

reformatted naming of output file

1c2d556

renamed genome_statistics directory to genome_note and added in the g…

c942d51

…enome_note template file

changed output for statistics table and completed genome note templat…

8b82728

…e to be wriiten to a results folder called genome_note

rmoved print statement

1936f29

passsed meta data through in the standard way

c143f0e

changed the way that meta data is handled

525559f

changed how meta data gets passed to the combine_metadata module

150151c

changed tag to include meta.id

8054f9e

fixed linting

2fc66aa

Merge pull request #70 from sanger-tol/genome_metadata

aa44b41

Genome metadata added module to produce a docx file from a genome note template file and genome metadata parameter file

edited to match style used elsewhere in the document

b6c21ed

write parameter values to the genome notes portal as an optional proc…

fce26ee

…ess. requires a secret to be set defining a key for the portal API

Set params for writing to database in test configs

71c70ab

fixed linting issues

afc0cb5

fixed linting

969ba33

fixed linting

cb69c23

Added usage instructions for setting nextflow secret for storing API …

f9adca0

…key to access genome notes database

fixed linting

4531bd0

added fix from ncbi branch

a622254

Merge pull request #75 from sanger-tol/genome_metadata

85f0462

Genome metadata

merged public_dev into update_higlass

588f9fd

merge in stashed changes

939f08e

merge stashed files

50fb922

config changes

a53c18e

BethYates and others added 25 commits October 8, 2024 07:17

linting fixes

19c1710

No longer have params.species so need to set value in meta correctly

e280a88

typo

c48817c

changes required as no longer have params.species

02b7dda

updates ahead of release

3b10acc

Update CHANGELOG.md

07cfc1c

increase default memory for POPULATE_TEMPLATE

93e3c33

With 50MB I was having it fail and re-try

remove duplicate container directive

f0f13ed

first directive is overwritten by second one, have tested that 2nd is correct! :)

Change to same container as other requests module

7642cf1

One less container to fetch; have tested

Don't upload to Higlass in full test

b6a3098

used elif rather than lots of ifs in parsing scripts, handle collecti…

f8f027c

…on_location parsing/matching better and include all linked assemblies

Merge branch 'release_2.0_fixes' of github.com:sanger-tol/genomenote …

4dc6f03

…into release_2.0_fixes

black fix

9414f63

fixed extending meta

a5eb096

add required parameters

7257505

simplify meta setting

7013322

added comments and appropriate error raising

2dff231

Moved sanger specific running instructions to the end of the file

8eb93d9

prettier fix

a896521

Fix KeyError Exceptions and ensure getting all biosample collectors/i…

e873d30

…dentifiers for the author string

black fixes

efc6169

Merge pull request #144 from sanger-tol/release_2.0_fixes

ddafa1e

Release 2.0 fixes

changed release data

0ef1ea9

Merge pull request #145 from sanger-tol/public_dev

73375e6

Release 2.0

bump version

5a54958

BethYates requested a review from muffato October 10, 2024 13:36

tkchafin approved these changes Oct 10, 2024

View reviewed changes

muffato approved these changes Oct 10, 2024

View reviewed changes

BethYates merged commit d0ec90c into main Oct 10, 2024
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Release 2.0.0 #146

Release 2.0.0 #146

BethYates commented Oct 10, 2024

github-actions bot commented Oct 10, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Release 2.0.0 #146

Release 2.0.0 #146

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BethYates commented Oct 10, 2024

PR checklist

github-actions bot commented Oct 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Oct 10, 2024 •

edited

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