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Fix workflow issues (except linting) #14

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Merged
KevinMenden merged 11 commits into from
Nov 16, 2020
Merged

Fix workflow issues (except linting) #14

KevinMenden merged 11 commits into from
Nov 16, 2020

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@KevinMenden KevinMenden commented Nov 16, 2020

This PR fixes the issue with the CI workflows
It doesn't fix the linting issue

@KevinMenden KevinMenden merged commit 3333acb into master Nov 16, 2020
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github-actions bot commented Nov 16, 2020 •
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nf-core lint overall result: Failed ❌

Updated for pipeline commit 4b6de8b

+| ✅ 59 tests passed       |+
!| ❗  0 tests had warnings |!
-| ❌  1 tests failed       |-
Details

❌ Test failures:

  • Test #5 - GitHub Actions 'branch' workflow should be triggered for PRs to master: /home/runner/work/testpipeline/testpipeline/.github/workflows/branch.yml

✅ Tests passed:

  • Test #1 - File found: nextflow.config
  • Test #1 - File found: nextflow_schema.json
  • Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • Test #1 - File found: README.md
  • Test #1 - File found: CHANGELOG.md
  • Test #1 - File found: docs/README.md
  • Test #1 - File found: docs/output.md
  • Test #1 - File found: docs/usage.md
  • Test #1 - File found: .github/workflows/branch.yml
  • Test #1 - File found: .github/workflows/ci.yml
  • Test #1 - File found: .github/workflows/linting.yml
  • Test #1 - File found: main.nf
  • Test #1 - File found: environment.yml
  • Test #1 - File found: Dockerfile
  • Test #1 - File found: conf/base.config
  • Test #1 - File found: .github/workflows/awstest.yml
  • Test #1 - File found: .github/workflows/awsfulltest.yml
  • Test #1 - File not found check: Singularity
  • Test #1 - File not found check: parameters.settings.json
  • Test #1 - File not found check: bin/markdown_to_html.r
  • Test #1 - File not found check: .travis.yml
  • Test #3 - Licence check passed
  • Test #2 - Dockerfile check passed
  • Test #4 - Config variable found: manifest.name
  • Test #4 - Config variable found: manifest.nextflowVersion
  • Test #4 - Config variable found: manifest.description
  • Test #4 - Config variable found: manifest.version
  • Test #4 - Config variable found: manifest.homePage
  • Test #4 - Config variable found: timeline.enabled
  • Test #4 - Config variable found: trace.enabled
  • Test #4 - Config variable found: report.enabled
  • Test #4 - Config variable found: dag.enabled
  • Test #4 - Config variable found: process.cpus
  • Test #4 - Config variable found: process.memory
  • Test #4 - Config variable found: process.time
  • Test #4 - Config variable found: params.outdir
  • Test #4 - Config variable found: params.input
  • Test #4 - Config variable found: manifest.mainScript
  • Test #4 - Config variable found: timeline.file
  • Test #4 - Config variable found: trace.file
  • Test #4 - Config variable found: report.file
  • Test #4 - Config variable found: dag.file
  • Test #4 - Config variable found: process.container
  • Test #4 - Config variable (correctly) not found: params.version
  • Test #4 - Config variable (correctly) not found: params.nf_required_version
  • Test #4 - Config variable (correctly) not found: params.container
  • Test #4 - Config variable (correctly) not found: params.singleEnd
  • Test #4 - Config variable (correctly) not found: params.igenomesIgnore
  • Test #4 - Config timeline.enabled had correct value: true
  • Test #4 - Config report.enabled had correct value: true
  • Test #4 - Config trace.enabled had correct value: true
  • Test #4 - Config dag.enabled had correct value: true
  • Test #4 - Config manifest.name began with nf-core/
  • Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
  • Test #4 - Config dag.file ended with .svg
  • Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
  • Test #4 - Config process.container looks correct: nfcore/testpipeline:dev
  • Test #4 - Config manifest.version ends in dev: '1.0dev'
  • Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/testpipeline/testpipeline/.github/workflows/branch.yml

Run details:

  • nf-core/tools version 1.11
  • Run at 2020-11-16 07:39:46

@ewels ewels deleted the dev branch March 16, 2021 09:28
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4 participants

@KevinMenden @ewels @ggabernet