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Fixes MISO scratch/launch directory and gffread issue #80

Merged
merged 5 commits into from
Jul 21, 2023
Merged

Fixes MISO scratch/launch directory and gffread issue #80

merged 5 commits into from
Jul 21, 2023

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jma1991
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@jma1991 jma1991 commented Jul 20, 2023

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/rnasplice 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).

@jma1991 jma1991 closed this Jul 20, 2023
@jma1991 jma1991 reopened this Jul 20, 2023
@jma1991
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jma1991 commented Jul 20, 2023

Hi @dkoppstein - please could you sync your fork with the latest dev? That should remove the 'branch has conflicts' message and allow me to merge into dev. Alternatively, I can quickly take your edits and push them from my fork.

@dkoppstein
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@jma1991 Just updated!

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github-actions bot commented Jul 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e06c05b

+| ✅ 155 tests passed       |+
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-21 08:25:14

@jma1991 jma1991 merged commit 85631a2 into nf-core:dev Jul 21, 2023
22 checks passed
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jma1991 commented Jul 21, 2023

Thanks for the PR @dkoppstein!

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@jma1991 @dkoppstein