Release 2.0 #16

muffato · 2024-05-23T17:19:32Z

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).

…ml template

Fix email html template

Remove email for notification and retry

only run when release or manual

to manaully run test on Sanger LSF

trigger the full test workflow when push to main or dev

update the wrong event name for push

update the work and results directory name

update outdir and work directory name

using variables for out and work dir

using variable for our and work dir

LSF full test

…ative paths from the samplesheet to the --outdir parameter

Template update

…facts

Use the latest version of the Tower action

New tolsoft details

Rework of the output directories

github-actions · 2024-05-23T17:20:51Z

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

Posted for pipeline commit 8976796

+| ✅ 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-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/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-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 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 (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: 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 08:12:16

gq1 · 2024-06-03T13:47:10Z

Can you merge this PR to dev branch as well?
#18

Ci branch check to main not master

muffato · 2024-06-03T17:39:46Z

Done

muffato and others added 30 commits October 7, 2022 17:00

.first() is not needed

6615371

Version bump

cf0e48f

add missing light logo image in assets directory

b63474e

resize logo image size in html email

cd0c710

reduce the logo image furthrer and show the full size in the email ht…

ba63ceb

…ml template

Merge pull request #3 from sanger-tol/fix-email-html-template

0695970

Fix email html template

Create tower_lsf_full_tests.yml

6c418ed

Update tower_lsf_full_tests.yml

33e89e3

Remove email for notification and retry

Update and rename tower_lsf_full_tests.yml to sangerfulltest.yml

6a8820f

only run when release or manual

Create sangertest.yml

afd58b6

to manaully run test on Sanger LSF

Update sangerfulltest.yml

f0f1c95

trigger the full test workflow when push to main or dev

Update sangerfulltest.yml

10416fc

update the wrong event name for push

Update sangerfulltest.yml

2bacd5e

update the work and results directory name

Update sangertest.yml

be81880

update outdir and work directory name

Update sangertest.yml

af7588a

using variables for out and work dir

Update sangerfulltest.yml

91dcc6a

using variable for our and work dir

Merge pull request #4 from sanger-tol/LSF_Full_test

e02c7ae

LSF full test

Updated logo

858714b

Support compressed files too

d2e1045

Imported the latest shared subworkflows

8ac8ff2

Reordering of parameters to match the other pipelines and connect rel…

0f538f9

…ative paths from the samplesheet to the --outdir parameter

Exclude the gene annotation files from md5checksums.txt

b0212c4

Provide a default value for --outdir

1c292c4

[prettier]

51437fd

nf-core lint fixes

9d4c07d

Pin nf-core to 2.5 since that is the version of the template I used

5d2f67e

--outdir is now mandatory

cf19126

Updated the change-log

9bb76be

Doc update

d2b5de9

bugfix: was discarding species_dir

631688c

muffato and others added 14 commits August 11, 2023 10:42

Merge pull request #10 from sanger-tol/template_update

aa2a366

Template update

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

1b7f285

Use the latest version of the Tower action

9f16631

Update sanger_test_full.yml, remove variable pipeline and upload arti…

b4eb799

…facts

Update sanger_test.yml - remove pipeline variable and upload artifacts

4fee623

Update sanger_test.yml

706a599

Update sanger_test_full.yml

231a097

Update sanger_test.yml

b2c6f82

Merge pull request #13 from sanger-tol/tower_action

24319dc

Use the latest version of the Tower action

New tolsoft details

9c20644

Fixed the repository name

c2dba62

Merge pull request #14 from sanger-tol/new_tolsoft_details

93a07cf

New tolsoft details

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

403f469

Merge pull request #12 from sanger-tol/outdir

5649f47

Rework of the output directories

Version bump

ffe15b9

muffato self-assigned this May 24, 2024

muffato added the enhancement Improvement of the existing features label May 24, 2024

[prettier]

21c81bf

This was referenced May 24, 2024

Release 2.0 sanger-tol/ensemblrepeatdownload#11

Merged

Release 2.0 sanger-tol/ensemblgenedownload#11

Merged

gq1 added 2 commits June 3, 2024 14:33

The default branch in main now, PR to main will fail, not master

6b71ac3

Add one more unchanged file for nf-core linting

8ee7114

Merge pull request #18 from sanger-tol/ci_branch

e79c6b7

Ci branch check to main not master

gq1 approved these changes Jun 3, 2024

View reviewed changes

Updated the release date

8976796

muffato merged commit 39d3f3d into main Jun 4, 2024
13 checks passed

tkchafin mentioned this pull request Jul 3, 2024

ERROR with tabix_selector in PREPARE_REPEATS subworkflow #22

Closed

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Release 2.0 #16

Release 2.0 #16

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 #16

Release 2.0 #16

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 ✅ ⚠️