Release 0.5 #104

muffato · 2024-07-10T16:25:48Z

The sum of four pull-requests: #98 #100 #99 #103

PR checklist

run the full test when push to dev or main branch

Large Tower Compute Env for CI jobs on farm

Co-authored-by: Guoying Qi <[email protected]>

Overall clean up

CI branch PR checking

All we need is Python and the yaml package

Publish peripheral data as well, even if we don't use it ourselves

github-actions · 2024-07-10T16:27:21Z

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

Posted for pipeline commit 544c135

+| ✅ 133 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.5.0

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_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: 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: CODE_OF_CONDUCT.md
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/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/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
template_strings - template_strings
merge_markers - merge_markers

✅ 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/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: lib/WorkflowBlobtoolkit.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: 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-blobtoolkit_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.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 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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md 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.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_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 - .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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
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: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.11
Run at 2024-07-31 17:38:13

More bugfixes

BethYates

Other than adding the release date to the change log file this looks good to me

pass quoteoption to splitCSV operator to allow handling of samplesheets from fetchngs which use double quotes around values.

Added fix to fetchngs samplesheet parsing in INPUT_CHECK.nf

Fix split csv in fetch input.nf

gq1 and others added 30 commits February 13, 2024 18:56

Update sanger_test.yml - use large tower env

0d4c6e7

Update sanger_test_full.yml - use large tower env

1bf0d25

Update sanger_test.yml - just add the push condition won't work

2eea140

Update sanger_test_full.yml

4992f1c

run the full test when push to dev or main branch

Merge pull request #93 from sanger-tol/large_tower_env

c36fb21

Large Tower Compute Env for CI jobs on farm

Merge branch 'main' into dev

acbc472

Skip the subworkflow if the nohit list is empty

305f87a

Fixed the documentation

2737952

Increased the resources for blastn

948e139

Version bump

a25e4bb

Removed an unused parameter

162b5fa

Removed trailing whitespace

afb27d3

Channel.of(...).first() is the same as Channel.value(...)

4a226cf

The accession is not appropriate there

0b12ad4

Removed some parameters that could in fact not be changed

043a120

The accession number is in fact mutually exclusive of the yaml file

5670deb

This should be value channel

083dbb8

Improved the type and handling of the busco_db channel

9e36a7a

Nicer name, even for compressed files

5c99602

This module is not used

b0e4e57

typo

9b1ecc3

Co-authored-by: Guoying Qi <[email protected]>

Merge pull request #98 from sanger-tol/clean_params

6581abf

Overall clean up

update the default branch from master to main for PR checking

b3c852c

Add one more unchanged file for nf-core linting

01c7d66

Merge pull request #100 from sanger-tol/ci_branch

d16a4df

CI branch PR checking

bugfix: this should be a megablast

2ae99f6

diamond blast should run with the --taxon-exclude option

cfac699

Publish peripheral data as well, even if we don't use it ourselves

c5da99d

Updated the documentation

e4b63a8

true is not needed

075dce3

muffato added 6 commits July 1, 2024 17:09

Switched to the default btk biocontainers because the pacbio one is gone

aef0532

All we need is Python and the yaml package

Merge pull request #99 from sanger-tol/more_published_files

7547ead

Publish peripheral data as well, even if we don't use it ourselves

Ignore the missing taxon_id errors issues when -negative_taxids is set

db3e317

CHANGELOG

8cfe4e5

blastn needs a bit more memory

93260b1

Adjusted the resources (incl. runtime) of blastn

310a812

muffato marked this pull request as draft July 10, 2024 16:26

muffato self-assigned this Jul 10, 2024

muffato added 2 commits July 15, 2024 09:23

There are blast failures we don't know how to fix. Just ignore for now

b83f05c

Merge pull request #103 from sanger-tol/more_bugfixes

5420de2

More bugfixes

muffato marked this pull request as ready for review July 18, 2024 19:55

muffato requested a review from BethYates July 18, 2024 19:56

BethYates approved these changes Jul 22, 2024

View reviewed changes

BethYates and others added 4 commits July 30, 2024 13:40

Update input_check.nf

0809ce0

pass quoteoption to splitCSV operator to allow handling of samplesheets from fetchngs which use double quotes around values.

Update CHANGELOG.md

a8e2bba

Added fix to fetchngs samplesheet parsing in INPUT_CHECK.nf

Merge pull request #107 from sanger-tol/fix_splitCsv_in_fetch_input.nf

50e5431

Fix split csv in fetch input.nf

Update the release date

544c135

muffato merged commit 1c0bf53 into main Jul 31, 2024
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Release 0.5 #104

Release 0.5 #104

muffato commented Jul 10, 2024 •

edited

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github-actions bot commented Jul 10, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

BethYates left a comment

Release 0.5 #104

Release 0.5 #104

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muffato commented Jul 10, 2024 • edited Loading

PR checklist

github-actions bot commented Jul 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

BethYates left a comment

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muffato commented Jul 10, 2024 •

edited

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github-actions bot commented Jul 10, 2024 •

edited

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