Patch release: 1.1.6 #469

LilyAnderssonLee · 2024-04-11T11:21:37Z

Patch release: 1.1.6

PR checklist

Co-authored-by: James A. Fellows Yates <[email protected]>

Bump up the pipeline version number in the dev branch

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

… path and directory

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

remove commented code about unique db_name check

Replace the db_params:null into empty string "".

Add meta.single_end to ch_input.nanopore channel

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

Logo fix

correct nanopore and fasta input channel - branch "dev"

Fix combine

github-actions · 2024-04-11T11:23:55Z

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

Posted for pipeline commit e805e26

+| ✅ 192 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.6
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ 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-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: 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-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: 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/WorkflowTaxprofiler.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://raw.githubusercontent.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.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.kmcp_mode= 3
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.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
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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 - .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 (264 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.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 2024-04-16 08:46:31

bump the version

Fix download pipeline workflow

LilyAnderssonLee · 2024-04-15T08:13:01Z

According to the these comments , the failing download-pipeline step will be ignore for now.

maxulysse · 2024-04-15T08:17:02Z

According to the these comments , the failing download-pipeline step will be ignore for now.

or you can remove -stub from the workflow, but then the tests take forever

LilyAnderssonLee · 2024-04-15T08:23:34Z

@maxulysse I'd prefer to leave it as is for now and address it in the next major release.

jfy133 · 2024-04-15T12:56:22Z

According to the these comments , the failing download-pipeline step will be ignore for now.

or you can remove -stub from the workflow, but then the tests take forever

Remove -stub but run the test_nothing profile?

LilyAnderssonLee · 2024-04-15T13:42:04Z

@jfy133 Should I fix it with your suggestion before this merge?

jfy133 · 2024-04-15T15:21:49Z

@jfy133 Should I fix it with your suggestion before this merge?

I think it would result in less changes that the current changes (but I can't really follow those changes 😬 )

But up to you!

maxulysse · 2024-04-16T07:53:29Z

Personally I don't like merging when tests are failing, so either I fix it, or I disable it.

Remove stub run in download_pipeline.yml

jfy133 · 2024-04-16T08:54:35Z

OK I think this would be OK now as Matthias says that there is no way around it until master is fixed!

sofstam and others added 30 commits February 8, 2024 10:41

Apply review suggestions

c2a15e2

Merge branch 'nf-core:dev' into dev

444d323

Bump to new dev version

154a219

Prettier

e04e613

Update CHANGELOG.md

7a86d96

Co-authored-by: James A. Fellows Yates <[email protected]>

Merge pull request #447 from genomic-medicine-sweden/bump_version

32a5539

Bump up the pipeline version number in the dev branch

Template update for nf-core/tools version 2.13

1041602

make full-pathed SVGs rather than text versions of the logos

9f33175

Include font-fullpath metromap

c3128c6

Template update for nf-core/tools version 2.13.1

53439cb

update the template and add nf-validation

b12a0bd

remove custom_dumpsoftwareversions

0310d75

Update .github/workflows/ci.yml

1c515f5

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update ci.yml

d5e6133

update error message in schema_databases.json

132a734

Update the db_path format definition to include both options for file…

5516e87

… path and directory

Update main.nf

7f9d873

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

Update assets/schema_database.json

af065d8

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

Update assets/schema_database.json

9389c31

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

Update assets/schema_database.json

596708b

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

update db_params in schema_databases.json

b730faa

Update taxprofiler.nf

c1e09b5

remove commented code about unique db_name check

Update taxprofiler.nf

bfe9aa8

Replace the db_params:null into empty string "".

Update taxprofiler.nf

54640ea

Add meta.single_end to ch_input.nanopore channel

Merge pull request #454 from nf-core/nf-core-template-merge-2.13.1

e81f171

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

Merge branch 'dev' of github.com:nf-core/taxprofiler into logo-fix

b90a05c

Merge pull request #453 from nf-core/logo-fix

91f61ea

Logo fix

correct nanopore and fasta input channel

1b3ce6b

Merge pull request #459 from LilyAnderssonLee/fix-validation-dev

9213006

correct nanopore and fasta input channel - branch "dev"

Try adding nextflow strict

4d6e111

Midnighter and others added 2 commits April 7, 2024 10:21

Merge pull request #464 from nf-core/fix-combine

a9afbc0

Fix combine

bump the version

eaaa9f2

LilyAnderssonLee requested review from sofstam and jfy133 April 11, 2024 11:21

Merge pull request #468 from LilyAnderssonLee/bump_version

bf48a1c

bump the version

LilyAnderssonLee requested review from nf-core-bot and removed request for jfy133 April 11, 2024 13:23

LilyAnderssonLee added 6 commits April 12, 2024 08:52

update download-pipeline.yml

04a2ba7

update download-pipeline.yml

06d2985

Merge pull request #470 from LilyAnderssonLee/fix-download-pipeline

89d4ca6

Fix download pipeline workflow

manully define stub run branch is master

8941b6e

update changelog and remove disk clean in download_pipeline.yml

2db93e4

Update download_pipeline.yml

39a66a3

LilyAnderssonLee requested a review from Midnighter April 12, 2024 13:24

LilyAnderssonLee mentioned this pull request Apr 12, 2024

Remove stub run in download_pipeline.yml #471

Merged

11 tasks

maxulysse approved these changes Apr 15, 2024

View reviewed changes

sofstam approved these changes Apr 15, 2024

View reviewed changes

remove stub run in download pipeline

8fe3968

Merge pull request #471 from LilyAnderssonLee/download-pipeline-bug

e805e26

Remove stub run in download_pipeline.yml

maxulysse approved these changes Apr 16, 2024

View reviewed changes

LilyAnderssonLee merged commit 45ce748 into master Apr 16, 2024
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Patch release: 1.1.6 #469

Patch release: 1.1.6 #469

LilyAnderssonLee commented Apr 11, 2024

github-actions bot commented Apr 11, 2024 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

LilyAnderssonLee commented Apr 15, 2024

maxulysse commented Apr 15, 2024

LilyAnderssonLee commented Apr 15, 2024

jfy133 commented Apr 15, 2024

LilyAnderssonLee commented Apr 15, 2024

jfy133 commented Apr 15, 2024

maxulysse commented Apr 16, 2024

jfy133 commented Apr 16, 2024

Patch release: 1.1.6 #469

Patch release: 1.1.6 #469

Conversation

LilyAnderssonLee commented Apr 11, 2024

PR checklist

github-actions bot commented Apr 11, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

LilyAnderssonLee commented Apr 15, 2024

maxulysse commented Apr 15, 2024

LilyAnderssonLee commented Apr 15, 2024

jfy133 commented Apr 15, 2024

LilyAnderssonLee commented Apr 15, 2024

jfy133 commented Apr 15, 2024

maxulysse commented Apr 16, 2024

jfy133 commented Apr 16, 2024

github-actions bot commented Apr 11, 2024 •

edited

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