Separate CI tests #349

LilyAnderssonLee · 2023-08-09T07:15:51Z

Fix the issue #314

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- [ ] If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
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).

Due to tower limitation producing ugly warning

Subsitute samtools/bam2fq with samtools/fastq

Co-authored-by: Sofia Stamouli <[email protected]>

Replace all instance of exit 1 with error for safety and consistency

BUmp Kraken2 nf-core module to prevent huge logs

Co-authored-by: Sofia Stamouli <[email protected]>

Add 'final reads for profiling' saving mechanism

Fix CENTRIFUGE header modification when --out-fmt turned on

The placement of the function is debatable, but to have its definition evaluated by nextflow, rather than pure Groovy makes it work.

@BenLangmead

Updated Bracken and Kraken2 database description to reflect the current contents on @BenLangmead database indexes. Also, required *.kraken from the expected files list for Bracken since they are no longer needed.

Updated Change Log to mention the usage update in PR #342

Update usage.md

Fix description

Function for mapcombinemultimap

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Add a tutorials page

github-actions · 2023-08-09T07:16:49Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @LilyAnderssonLee,

It looks like this pull-request is has been made against the LilyAnderssonLee/taxprofiler master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the LilyAnderssonLee/taxprofiler dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2023-08-09T07:19:40Z

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

Posted for pipeline commit d1694db

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ 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/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-taxprofiler_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-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_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: lib/nfcore_external_java_deps.jar
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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowTaxprofiler.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-taxprofiler_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.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 manifest.version ends in dev: 1.1.0dev
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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md 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-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png 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/NfcoreTemplate.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
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
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (194 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.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 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 2.9
Run at 2023-08-09 07:18:49

jfy133 and others added 30 commits April 4, 2023 11:19

Reduce authors to main + other contributors

1eeeb8a

Due to tower limitation producing ugly warning

Replace all instance of exit 1 with error for safety and consistency

03c3169

update CHAGENLGO

59f8d75

Update LICENSE

5eee462

Further fixes

ca9c0cf

More tweaks

e5e0aab

Mix reads in emit

c47b9e5

Everywhere account when no-runmerging for single libs

94e88d7

Add final documentation

ce97a11

Prettier

3f34603

Merge pull request #274 from sofstam/samtools_fastq

255b492

Subsitute samtools/bam2fq with samtools/fastq

Apply suggestions from code review

ee031eb

Co-authored-by: Sofia Stamouli <[email protected]>

Apply suggestions from code review

105bac7

Merge branch 'dev' into final-reads-saving

0245c48

Merge branch 'dev' into replace-exit-with-error

b3e602d

Logic safety!

5d90c77

Add team sectionb

f476b49

Make all saveAs conditions consistent

31e3c21

[automated] Fix linting with Prettier

4f7e2ee

BUmp Kraken2 nf-core module to prevent huge logs

0ed110c

MultiQC optimisations for DIAMOND and Falco

1eb9517

Update CHANGELOG

59f3146

Update README.md

d06ac37

Co-authored-by: Sofia Stamouli <[email protected]>

[automated] Fix linting with Prettier

386b1c9

Merge pull request #280 from nf-core/replace-exit-with-error

c3c9178

Replace all instance of exit 1 with error for safety and consistency

Merge pull request #285 from nf-core/update-kraken

003862d

BUmp Kraken2 nf-core module to prevent huge logs

Merge branch 'dev' into multiqc-optimisations

5a09319

Misssing changelog manual prettier [skip ci]

e000ac3

Update conf/modules.config

ee76a5f

Co-authored-by: Sofia Stamouli <[email protected]>

Merge pull request #272 from nf-core/final-reads-saving

2140928

Add 'final reads for profiling' saving mechanism

jfy133 and others added 27 commits July 27, 2023 15:09

Merge branch 'dev' into centrifuge-fix

3437201

Merge pull request #338 from nf-core/centrifuge-fix

fba2d8c

Fix CENTRIFUGE header modification when --out-fmt turned on

refactor: move function to nextflow module, rename

6c93c10

The placement of the function is debatable, but to have its definition evaluated by nextflow, rather than pure Groovy makes it work.

chore: clean up module

8d47f72

Merge branch 'dev' into function-for-mapcombinemultimap

3be05ce

Update usage.md

786f77f

Updated Bracken and Kraken2 database description to reflect the current contents on @BenLangmead database indexes. Also, required *.kraken from the expected files list for Bracken since they are no longer needed.

Update CHANGELOG.md

edd9811

Updated Change Log to mention the usage update in PR #342

Apply suggestions from code review

41969d4

[automated] Fix linting with Prettier

003828f

Merge pull request #342 from husensofteng/patch-1

2aed785

Update usage.md

Use function everywhwere

e38b36a

Fix description

7792834

Merge pull request #343 from nf-core/fix-description

6586940

Fix description

Merge pull request #339 from nf-core/function-for-mapcombinemultimap

7963917

Function for mapcombinemultimap

Add a tutorials page

af1ac42

Restructure docs

b0691b5

Add comment about interactive session

9e26b60

Apply suggestions from code review

9991283

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Replace all old info blocks (todo: warnings)

54cdead

Replace all emojis with warning admonitions

74ade9d

Use new tip admonation and fix after tutorial review

bab52fb

Apply suggestions from code review

951c238

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Fix linking and typo fixes

7f6ac78

Merge pull request #345 from nf-core/tutorials

a98d49b

Add a tutorials page

Seperate CI tests

8779ed1

Fix CI test

783660d

add test_malt

d1694db

LilyAnderssonLee closed this Aug 9, 2023

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Separate CI tests #349

Separate CI tests #349

LilyAnderssonLee commented Aug 9, 2023

github-actions bot commented Aug 9, 2023

github-actions bot commented Aug 9, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

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Separate CI tests #349

Separate CI tests #349

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LilyAnderssonLee commented Aug 9, 2023

PR checklist

github-actions bot commented Aug 9, 2023

This PR is against the master branch ❌

github-actions bot commented Aug 9, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

This PR is against the `master` branch ❌

github-actions bot commented Aug 9, 2023 •

edited

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