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Don't stash unexistent files #67

Merged
merged 1 commit into from
Aug 4, 2023
Merged

Don't stash unexistent files #67

merged 1 commit into from
Aug 4, 2023

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mirpedrol
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Previously when a file was null, we were trying to stash files called "null", this files don't exist, and this broke AWS tests. Now we are using empty lists instead, the propper way to handle null or empty channels in Nextflow.

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/crisprseq 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 3, 2023

nf-core lint overall result: Failed ❌

Posted for pipeline commit 1d111f9

+| ✅ 156 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-03 13:00:11

@mirpedrol mirpedrol merged commit d8d0935 into nf-core:dev Aug 4, 2023
@mirpedrol mirpedrol deleted the fix-null-files branch August 4, 2023 11:12
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@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

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@mirpedrol @LaurenceKuhl