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Pval param (1) #145

Merged
merged 14 commits into from
Sep 1, 2022
Merged

Pval param (1) #145

merged 14 commits into from
Sep 1, 2022

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WackerO
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@WackerO WackerO commented Aug 5, 2022 •
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Pval threshold can now be set, closes #138

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/rnadeseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Aug 5, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7dd2761

+| ✅ 116 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • 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.
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters

❔ 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 does not exist: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or foo

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-08-29 11:19:43

@WackerO WackerO changed the title Pval param Pval param (1) Aug 9, 2022
@WackerO WackerO changed the base branch from dev to master August 11, 2022 12:47
@WackerO WackerO changed the base branch from master to dev August 11, 2022 12:47
@WackerO WackerO marked this pull request as ready for review August 26, 2022 13:40
SusiJo
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@WackerO @SusiJo
Update nextflow_schema.json
7dd2761 
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
SusiJo
SusiJo approved these changes Sep 1, 2022
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LGTM @WackerO!

@WackerO WackerO merged commit bdc0857 into qbic-pipelines:dev Sep 1, 2022
@WackerO WackerO deleted the pval branch September 1, 2022 10:39
@WackerO WackerO mentioned this pull request Sep 5, 2022
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@WackerO WackerO mentioned this pull request Sep 13, 2022
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