Improve containers and NACHO 2.0.6 #58

apeltzer · 2024-01-16T10:20:36Z

PR checklist

github-actions · 2024-01-16T10:21:57Z

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

Posted for pipeline commit 711ceef

+| ✅ 162 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.2.1
pipeline_todos - TODO string in WorkflowNanostring.groovy: Optionally add in-text citation tools to this list.

✅ 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-nanostring_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-nanostring_logo_light.png
files_exist - File found: docs/images/nf-core-nanostring_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/WorkflowNanostring.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-nanostring_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 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 - 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-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_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 (93 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: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: awstest.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 2.11.1
Run at 2024-01-17 15:23:35

apeltzer · 2024-01-16T14:04:38Z

This is now ready for review @christopher-mohr

christopher-mohr · 2024-01-17T09:30:48Z

This is now ready for review @christopher-mohr

I will have a look later why the tests are failing.

apeltzer · 2024-01-17T10:09:09Z

Will just need this to pin matrixstats : BioContainers/multi-package-containers#2880

Adjust container with matrixstats one

apeltzer · 2024-01-17T13:47:40Z

@nf-core-bot fix linting pretty please

…anostring into granularize-containers

christopher-mohr

Just a couple of minor things.

.devcontainer/devcontainer.json

CHANGELOG.md

nextflow.config

assets/multiqc_config.yml

Co-authored-by: Christopher Mohr <[email protected]>

christopher-mohr · 2024-01-17T15:22:20Z

@nf-core-bot fix linting pretty please

christopher-mohr

LGTM

…anostring into granularize-containers

Cleaning up a bit

5c07755

apeltzer added 6 commits January 16, 2024 10:24

Fix ggplot2 imports

518f132

Attempt at fixing things

5a23113

Adding in readr

4517141

A bit more cleaning

a61dba9

Add column to rownames

2e0b213

Adding in tibble

fcac0d8

apeltzer requested a review from christopher-mohr January 16, 2024 14:04

apeltzer added 3 commits January 16, 2024 14:19

improve version logging substantially

7d0c688

Updated mulled container with tidyr

1f210d8

Hopefully fixing things

e81331c

Run matrixstats

b9191ae

Update compute_gene_scores.nf

28f8552

Adjust container with matrixstats one

nf-core-bot and others added 3 commits January 17, 2024 13:47

[automated] Fix linting with Prettier

6980075

Merge branch 'granularize-containers' of https://github.com/nf-core/n…

78dcf12

…anostring into granularize-containers

Bump 1.2.1 for new release

055814f

christopher-mohr requested changes Jan 17, 2024

View reviewed changes

.devcontainer/devcontainer.json Show resolved Hide resolved

CHANGELOG.md Show resolved Hide resolved

nextflow.config Show resolved Hide resolved

assets/multiqc_config.yml Show resolved Hide resolved

CHANGELOG.md aktualisieren

9688cdc

Co-authored-by: Christopher Mohr <[email protected]>

[automated] Fix linting with Prettier

711ceef

christopher-mohr approved these changes Jan 17, 2024

View reviewed changes

apeltzer added 2 commits January 17, 2024 15:39

[skip ci] adjust heatmap title

a0fe70e

Merge branch 'granularize-containers' of https://github.com/nf-core/n…

02f5418

…anostring into granularize-containers

apeltzer merged commit ec27288 into dev Jan 17, 2024
6 checks passed

apeltzer deleted the granularize-containers branch January 17, 2024 15:41

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Improve containers and NACHO 2.0.6 #58

Improve containers and NACHO 2.0.6 #58

apeltzer commented Jan 16, 2024

github-actions bot commented Jan 16, 2024 •

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❗ Test warnings:

✅ Tests passed:

Run details

apeltzer commented Jan 16, 2024

christopher-mohr commented Jan 17, 2024

apeltzer commented Jan 17, 2024

apeltzer commented Jan 17, 2024

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Improve containers and NACHO 2.0.6 #58

Improve containers and NACHO 2.0.6 #58

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apeltzer commented Jan 16, 2024

PR checklist

github-actions bot commented Jan 16, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

apeltzer commented Jan 16, 2024

christopher-mohr commented Jan 17, 2024

apeltzer commented Jan 17, 2024

apeltzer commented Jan 17, 2024

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github-actions bot commented Jan 16, 2024 •

edited

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