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Add missing stubs #1139

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Add missing stubs #1139

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bentsherman
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Adds a few stubs that were missing. Basically just creates the minimum set of output files required to achieve a successful run. Likely could be made more detailed like the existing stubs so that the stub run is closer to an actual run in terms of tasks executed.

PR checklist

  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@bentsherman
Add missing stubs
fed0892 
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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github-actions bot commented Dec 13, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fed0892

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-13 15:40:57

@pinin4fjords
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Thanks @bentsherman ! The nf-core ones will have to go via the modules repo though

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@bentsherman @pinin4fjords