Release v2.1.1 #83

asp8200 · 2024-03-13T14:10:59Z

Once approved and merged to master, I'll make release/tag on GitHub.

The awsmegatests test and test_full have been executed from the dev-branch (db5efc6):

https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2JIQCvLrzsr2Tt

https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3cNYNEzOs9H8Fj

PR checklist

To (partially?) address #63.

tweak usage.md

Important! Template update for nf-core/tools v2.12

Update samtools

…ve_conflicts Nf core template merge 2.13 resolve conflicts

Important! Template update for nf-core/tools v2.13.1

Update changelog for release v2.1.1

github-actions · 2024-03-13T14:12:11Z

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

Posted for pipeline commit 49e9b0a

+| ✅ 168 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.1.1
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ 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: 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/config.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: assets/nf-core-bamtofastq_logo_light.png
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/images/nf-core-bamtofastq_logo_light.png
files_exist - File found: docs/images/nf-core-bamtofastq_logo_dark.png
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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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: pipeline_template.yml
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-bamtofastq_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: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowBamtofastq.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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://github.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.reads_in_memory= 100000
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://github.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.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 - .github/workflows/linting.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 - assets/nf-core-bamtofastq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bamtofastq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bamtofastq_logo_dark.png matches the template
files_unchanged - docs/README.md 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
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (166 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: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
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 2.13.1
Run at 2024-05-06 08:50:59

Removing option stub from CI-test of download

.github/CONTRIBUTING.md

main.nf

maxulysse

Looking good, I think we're quite close to a release

Import fasta_fai in main.nf

main.nf

matthdsm

LGTM, but wait for another reviewer

maxulysse · 2024-05-06T08:19:54Z

@asp8200
#88 will fix the failing test

feat(subworkflow): update utils_nfcore_pipeline

allaway and others added 30 commits October 13, 2023 15:08

tweak usage.md

6ef61ef

To (partially?) address #63.

Update usage.md

539f54b

Update usage.md

dac1e31

consistency of colnames

f7be719

[automated] Fix linting with Prettier

9bf7b9a

Merge pull request #68 from allaway/dev

b4c15ee

tweak usage.md

Template update for nf-core/tools version 2.11

e5fc18d

Template update for nf-core/tools version 2.11.1

c4cf474

Template update for nf-core/tools version 2.12

5400508

update samtools

09ab01e

update tests

7fd7f8d

Merge branch 'dev' into nf-core-template-merge-2.12

3dd5b17

fix nf-core lint

4d695ce

Merge pull request #73 from nf-core/nf-core-template-merge-2.12

1543f81

Important! Template update for nf-core/tools v2.12

Merge branch 'nf-core:master' into update_samtools

abf3f94

Adding fasta_fai input-channel in call to SAMTOOLS_STATS

0695ecb

Handling input-channels of tuples including meta

f102b4e

removing docker.userEmulation from nextflow.config

8d238d5

Merge pull request #74 from asp8200/update_samtools

3122b17

Update samtools

Template update for nf-core/tools version 2.13

5492540

update all modules

6a88686

tests and environment.yml for cat/fastq

7547723

Fixing #22

8103265

Merging dev-branch into template

254d231

Template update for nf-core/tools version 2.13.1

b741444

Merge pull request #78 from asp8200/nf-core-template-merge-2.13_resol…

c1a9383

…ve_conflicts Nf core template merge 2.13 resolve conflicts

Merge branch 'dev' into nf-core-template-merge-2.13.1

b559a1c

Update nextflow.config

7915a0d

Merge pull request #80 from nf-core/nf-core-template-merge-2.13.1

f6c5b10

Important! Template update for nf-core/tools v2.13.1

Merge branch 'dev' into fix_22

35af2c4

asp8200 and others added 2 commits March 13, 2024 13:40

Ran nf-core bump-version

851a626

Merge pull request #82 from nf-core/update_changelog

008854c

Update changelog for release v2.1.1

asp8200 and others added 4 commits March 13, 2024 15:20

Removing option stub from CI-test of download

54a8e8a

Updating changelog

98ce868

update changelog

795889b

Merge pull request #84 from nf-core/fix_download_test

e96b009

Removing option stub from CI-test of download

asp8200 marked this pull request as ready for review March 13, 2024 19:08

asp8200 requested review from maxulysse, SusiJo and FriederikeHanssen March 13, 2024 19:14

maxulysse reviewed Mar 15, 2024

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asp8200 added 4 commits March 15, 2024 20:36

impot fasta_fai

2aef0e2

remove redundant definition of fasta_fai

bd05f59

Remove comment

7a5ee93

Revert to former msg concerning tests

32487a8

asp8200 mentioned this pull request Mar 15, 2024

Import fasta_fai in main.nf #85

Merged

10 tasks

Merge pull request #85 from asp8200/import_fasta_fai

db5efc6

Import fasta_fai in main.nf

asp8200 requested a review from maxulysse May 2, 2024 09:35

maxulysse reviewed May 2, 2024

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matthdsm approved these changes May 2, 2024

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Update main.nf

f071dfe

maxulysse approved these changes May 6, 2024

View reviewed changes

maxulysse and others added 2 commits May 6, 2024 10:22

feat(subworkflow): update utils_nfcore_pipeline

bf98197

Merge pull request #88 from maxulysse/utils_nfcore_pipeline

49e9b0a

feat(subworkflow): update utils_nfcore_pipeline

asp8200 merged commit 38fdb8b into master May 6, 2024
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Release v2.1.1 #83

Release v2.1.1 #83

asp8200 commented Mar 13, 2024 •

edited

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github-actions bot commented Mar 13, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

matthdsm left a comment

maxulysse commented May 6, 2024 •

edited

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Release v2.1.1 #83

Release v2.1.1 #83

Conversation

asp8200 commented Mar 13, 2024 • edited Loading

PR checklist

github-actions bot commented Mar 13, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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maxulysse commented May 6, 2024 • edited Loading

asp8200 commented Mar 13, 2024 •

edited

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github-actions bot commented Mar 13, 2024 •

edited

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

maxulysse commented May 6, 2024 •

edited

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