Template update (6) by WackerO · Pull Request #163 · qbic-pipelines/rnadeseq

WackerO · 2022-09-26T12:35:40Z

This PR does another template update

PR checklist

… template_update

github-actions · 2022-09-26T12:37:29Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit d71f4c0

+| ✅ 118 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗  11 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ Test failures:

files_unchanged - lib/NfcoreTemplate.groovy does not match the template
actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

files_exist - File not found: pyproject.toml
readme - README did not have a Nextflow minimum version badge.
readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
schema_lint - Parameter input not found in schema

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
files_exist - File is ignored: bin/markdown_to_html.r
files_exist - File is ignored: .github/workflows/push_dockerhub.yml
files_exist - File is ignored: assets/multiqc_config.yaml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: lib/WorkflowQbic-pipelines/rnadeseq.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.input
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/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.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/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ 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-rnadeseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: docs/images/nf-core-rnadeseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnadeseq_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/NfcoreSchema.groovy
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: lib/WorkflowRnadeseq.groovy
files_exist - File found: modules.json
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: conf/aws.config
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-rnadeseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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.version
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 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 manifest.version ends in dev: '2.1.0dev'
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 - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (128 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: push_dockerhub.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 'export_plots: true'.

Run details

nf-core/tools version 2.5.1
Run at 2022-09-26 12:37:14

ggabernet

After applying the review comments it looks good to me. Maybe also the fastqc and multiqc added modules can be removed

changed; this seems to be not specific to this PR, rather the output from running the pipeline on the master branch also reflects these changes!

…into template_update

batcheffect is once again totally unstable...

packages to env (limma, annotationdbi, colorbrewr), added packages to assets/RNAseq_report.Rmd to specify from which package a function should be importet so people can see that these packages are still used

…condaforge/mambaforge

WackerO added 3 commits September 7, 2022 14:06

Initial template commit

6fbc382

Merge branch 'TEMPLATE' into dev

97d37dd

Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…

d71f4c0

… template_update

WackerO marked this pull request as ready for review November 3, 2022 07:50

WackerO requested a review from ggabernet November 3, 2022 07:50

WackerO changed the title ~~Template update~~ Template update (6) Nov 3, 2022

ggabernet changed the base branch from dev to master November 4, 2022 12:08

ggabernet changed the base branch from master to dev November 4, 2022 12:08

Added newline to restart github tests

8fbe0f2

ggabernet approved these changes Nov 4, 2022

View reviewed changes

Comment thread assets/samplesheet.csv Outdated

Comment thread conf/test_full.config Outdated

WackerO and others added 10 commits November 8, 2022 13:49

Fixed pytests. Note that the query results from gprofiler2 seem to have

116aeb3

changed; this seems to be not specific to this PR, rather the output from running the pipeline on the master branch also reflects these changes!

Merge branch 'dev' into template_update

afe128a

Removed hard-coded write command...

2a776fc

Merge branch 'template_update' of https://github.com/WackerO/rnadeseq …

4092cda

…into template_update

Removed some obsolete files

7a39a1c

Changed some md5sums and fixed some file names

0e5be44

Changed batcheffect 5sums back. If this changes again, just merge,

a28578f

batcheffect is once again totally unstable...

Switched docker container to mamba, re-added incorrectly deleted

7ef8247

packages to env (limma, annotationdbi, colorbrewr), added packages to assets/RNAseq_report.Rmd to specify from which package a function should be importet so people can see that these packages are still used

Switched Dockerfile to mamba instead of conda; base container is now …

06e2497

…condaforge/mambaforge

Updated rsem 5sums (only minor decimal differences)

ec4d43a

WackerO merged commit 11426cc into qbic-pipelines:dev Nov 23, 2022

WackerO deleted the template_update branch November 23, 2022 14:12

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Template update (6)#163

Template update (6)#163
WackerO merged 14 commits intoqbic-pipelines:devfrom
WackerO:template_update

WackerO commented Sep 26, 2022 •

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github-actions Bot commented Sep 26, 2022 •

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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WackerO commented Sep 26, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR checklist

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github-actions Bot commented Sep 26, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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WackerO commented Sep 26, 2022 •

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github-actions Bot commented Sep 26, 2022 •

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`nf-core lint` overall result: Failed ❌