Species library fix (5) by WackerO · Pull Request #150 · qbic-pipelines/rnadeseq

WackerO · 2022-08-10T10:45:26Z

This PR fixes the error with the installation of the species library and also removes human and mouse from the env.yml as both are now installed as required; closes #142.

PR checklist

github-actions · 2022-08-10T10:45:39Z

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 @WackerO,

It looks like this pull-request is has been made against the WackerO/rnadeseq 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 WackerO/rnadeseq 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 · 2022-08-10T10:46:43Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 7d30253

+| ✅ 116 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

files_exist - File not found: .prettierignore
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
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.
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: .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 (120 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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 2022-09-12 09:22:25

… speclib

rsem and salmon for some reason

time...

forth between 2 5sums per file). If it does not work this time, I will comment them out for batcheffect

github does not manage to make the files consistent

ggabernet

Looks good to me, let's test the md5sum issue in a new PR where the container does not get rebuilt!

Fixed variabe species library

c951d95

WackerO marked this pull request as ready for review September 5, 2022 12:41

WackerO changed the base branch from master to dev September 5, 2022 13:29

WackerO added 6 commits September 5, 2022 15:35

Fixed some pytest errors

a97d655

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

947ec65

… speclib

Removed unnecessary force param from BiocManager

57429e6

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

e785dd5

… speclib

Updated changelog

d1d93ca

Added force=T again, it seems to be necessary after all, but only for

c657e47

rsem and salmon for some reason

WackerO requested a review from ggabernet September 6, 2022 13:21

WackerO added 6 commits September 6, 2022 15:26

Updated batch checksums

db128c9

Changed batch 5sums once again. Hopefully, they stay correct this

0d00b01

time...

Final change to the 5sums (I am literally just changing them back and

5d32ff4

forth between 2 5sums per file). If it does not work this time, I will comment them out for batcheffect

The first couple of md5sums for batcheffect are now commented out;

9b74619

github does not manage to make the files consistent

Simplified container definition

f943917

Reenabled checksums

7d30253

ggabernet approved these changes Sep 12, 2022

View reviewed changes

WackerO merged commit 3cc0976 into qbic-pipelines:dev Sep 12, 2022

WackerO mentioned this pull request Sep 13, 2022

Look again at species library #142

Closed

WackerO deleted the speclib branch December 20, 2022 11:55

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Species library fix (5)#150

Species library fix (5)#150
WackerO merged 13 commits intoqbic-pipelines:devfrom
WackerO:speclib

WackerO commented Aug 10, 2022 •

edited

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github-actions Bot commented Aug 10, 2022 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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WackerO commented Aug 10, 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 Aug 10, 2022

This PR is against the master branch ❌

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nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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WackerO commented Aug 10, 2022 •

edited

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This PR is against the `master` branch ❌

github-actions Bot commented Aug 10, 2022 •

edited

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`nf-core lint` overall result: Failed ❌