Release 1.1.0 to main branch #66

gq1 · 2023-12-17T12:59:13Z

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).

Merging main into dev after release

Updated CI

Our new convention is use per-pipeline directories under pipeline_info/

Use the latest version of the Tower action

…he full url of repo

Tower action version updating 2

Use the tolsoft access token to fix linting

* Use the same name as our GitHub user to allow linking * Use the same email as our GitHub user to allow linking * Renamed the secret for consistency * Allow running the action on this branch * Messed up with the indentation * fixup! Allow running the action on this branch * Hardcode the issue number to allow checking out the code * Wrong issue number * [automated] Fix linting with Prettier * Restored the original condition * Fixed wrong user name Co-authored-by: Guoying Qi <[email protected]> --------- Co-authored-by: sanger-tolsoft <[email protected]> Co-authored-by: Guoying Qi <[email protected]>

* TEMPLATE: Template update for nf-core/tools version 2.8 add pipeline template file # Conflicts: # .github/workflows/sanger_test.yml # .github/workflows/sanger_test_full.yml # .nf-core.yml # CHANGELOG.md # CITATIONS.md # LICENSE # README.md # assets/email_template.html # bin/check_samplesheet.py # docs/output.md # docs/usage.md # lib/WorkflowMain.groovy # modules.json # nextflow.config # pipeline_template.yml # workflows/variantcalling.nf

nf-core modules update deepvariant nf-core modules update custom/dumpsoftwareversions nf-core modules update cat/cat nf-core modules update bcftools/concat nf-core lint --fix files_unchanged ( nf-core 2.8)

wrong default value Co-authored-by: Matthieu Muffato <[email protected]>

Pacbio align

github-actions · 2023-12-17T13:01:12Z

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

Posted for pipeline commit 43aea20

+| ✅ 125 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.1.0'

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-variantcalling_logo_light.png
files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
files_exist - File is ignored: docs/images/nf-core-variantcalling_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: assets/multiqc_config.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/PULL_REQUEST_TEMPLATE.md
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/email_template.html
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.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: 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/WorkflowVariantcalling.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-variantcalling_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/workflows/linting_comment.yml 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 (150 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_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: ci.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 2023-12-20 10:46:08

Release1.1.0 - dev

gq1 · 2023-12-20T11:07:25Z

Sorry, I merged this one without waiting. All tests should be fine.

muffato · 2023-12-20T11:09:46Z

Everything should be fine 🤞🏼

priyanka-surana and others added 30 commits May 3, 2023 11:57

Merge pull request #38 from sanger-tol/main

0248662

Merging main into dev after release

The ".sandbox" pseudo-project is deprecated

bbdfc4f

Fixed a template error

683652f

Merge pull request #50 from sanger-tol/updated_ci

d55afb8

Updated CI

Our new convention is use per-pipeline directories under pipeline_info/

a3eb217

Merge pull request #51 from sanger-tol/pipeline_info

3363536

Our new convention is use per-pipeline directories under pipeline_info/

Latest nomenclature

3fc2c95

Use the latest version of the Tower action

571735a

Merge pull request #52 from sanger-tol/tower_action

a557d60

Use the latest version of the Tower action

Wrong version number and keep the tower log files

c8483ba

just a test

e876f6a

v2.0.0 doesn't work

4034b3e

using v2

808e073

delete the pipeline variable, using the default one - which will be t…

5f9589e

…he full url of repo

finish the test and put everything back to normal

6b23886

put back the version number as v2

8a7db40

Merge pull request #53 from sanger-tol/tower_action

bf29fa9

Tower action version updating 2

Use the tolsoft access token to fix linting

ebc3b22

Merge pull request #54 from sanger-tol/fix_linting_access_token

a5cb2d5

Use the tolsoft access token to fix linting

nf-core lint --fix files_unchanged ( nf-core 2.8)

febbcff

nf-core modules update bcftools/concat

5fc66d6

nf-core modules update cat/cat

3c7c11a

nf-core modules update custom/dumpsoftwareversions

bed2298

nf-core modules update deepvariant

c9b4e23

Add pipeline template yml file

025297e

add pipeline template file

7789085

Template update for nf-core/tools version 2.8

7a3aeb8

Modules updating:

2ddb943

nf-core modules update deepvariant nf-core modules update custom/dumpsoftwareversions nf-core modules update cat/cat nf-core modules update bcftools/concat nf-core lint --fix files_unchanged ( nf-core 2.8)

gq1 and others added 5 commits December 7, 2023 15:33

make sure fasta or fa being removed from the fasta file name

d348591

Update nextflow_schema.json

7d20b1d

wrong default value Co-authored-by: Matthieu Muffato <[email protected]>

change maxRetries to 5.

45a7ba4

Merge pull request #63 from sanger-tol/pacbio_align

5f528f7

Pacbio align

remove dev from the version

85215f5

gq1 added 2 commits December 18, 2023 20:22

Add mermaid gitgraph workflow diagram

5f4419f

increase commit label size

4522f72

gq1 changed the title ~~Dev~~ Release 1.1.0 to main Dec 19, 2023

gq1 changed the title ~~Release 1.1.0 to main~~ Release 1.1.0 to main branch Dec 19, 2023

gq1 and others added 14 commits December 19, 2023 14:25

mermaid code mainly markdown

ec4e8ee

change logs

c1dd0e3

update readme

ac88f50

update citations

0be537c

usage

34605be

output updated

b0b489a

update the mermaid file and images

60fbbc2

Updated the image

038517f

update usage.

af798af

Add a name for previous release

ce19b42

Add citation file

64eba1f

ignore cff file for EC lint check

c287ef7

typo

d3058e7

Merge pull request #67 from sanger-tol/release1.1.0

43aea20

Release1.1.0 - dev

gq1 marked this pull request as ready for review December 20, 2023 10:51

gq1 requested review from priyanka-surana and muffato December 20, 2023 10:51

gq1 merged commit 15a1475 into main Dec 20, 2023
14 checks passed

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Release 1.1.0 to main branch #66

Release 1.1.0 to main branch #66

gq1 commented Dec 17, 2023

github-actions bot commented Dec 17, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Dec 20, 2023

muffato commented Dec 20, 2023

Release 1.1.0 to main branch #66

Release 1.1.0 to main branch #66

Conversation

gq1 commented Dec 17, 2023

PR checklist

github-actions bot commented Dec 17, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Dec 20, 2023

muffato commented Dec 20, 2023

github-actions bot commented Dec 17, 2023 •

edited

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